Mercurial > repos > chemteam > gmx_fep

annotate alchemical_run/gmx_fep.xml @ 2:c1bcdba99bb3 draft default tip

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit eefe89bfcd6c3e98f4e774e508ad0659dcc2f65c"
author chemteam
date Sun, 01 Dec 2019 09:47:35 -0500
parents 19d1d4c30402
children
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0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
1 <tool id="gmx_fep" name="Alchemical Run" version="2019.1">
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
2 <description>Alchemical free energy simulations using gromacs</description>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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3 <requirements>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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4 <requirement type="package" version="2019.1">gromacs</requirement>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
5 </requirements>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
6 <command detect_errors="exit_code"><![CDATA[
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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7 ln -s '$em_steep' ./em_steep.mdp &&
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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8 ln -s '$nvt' ./nvt.mdp &&
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
9 ln -s '$npt' ./npt.mdp &&
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
10 ln -s '$md' ./md.mdp &&
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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11
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
12 ln -s '$groin' ./morph.gro &&
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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13 ln -s '$topin' ./morph.top &&
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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14
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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15 #if $input_fep == 'perform':
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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16 bash '$__tool_directory__/gmx_fep.sh' '$path.lambda' &>> '$report'
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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17 #end if
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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18 #if $input_fep == 'generate':
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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19 mkdir -p input_files &&
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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20 cp '$__tool_directory__/gmx_fep.sh' input_files/ &&
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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21 cp ./em_steep.mdp input_files/ &&
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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22 cp ./nvt.mdp input_files/ &&
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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23 cp ./npt.mdp input_files/ &&
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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24 cp ./md.mdp input_files/ &&
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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25 cp ./morph.gro input_files/ &&
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
26 cp ./morph.top input_files/ &&
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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27 tar cf input_files.tar input_files/
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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28 #end if
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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29 ]]></command>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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30 <configfiles>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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31 <configfile name="em_steep">
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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32 integrator = steep
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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33 nsteps = $minstep
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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34 emtol = 100
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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35 emstep = 0.01
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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36 niter = 20
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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37 nbfgscorr = 10
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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38 nstlog = 1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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39 nstenergy = 1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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40 cutoff-scheme = verlet
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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41 nstlist = 10
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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42 ns_type = grid
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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43 pbc = xyz
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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44 rlist = 1.2
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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45 coulombtype = PME
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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46 rcoulomb = 1.2
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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47 vdwtype = cutoff
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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48 vdw-modifier = potential-switch
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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49 rvdw-switch = 1.0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
50 rvdw = 1.2
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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51 DispCorr = EnerPres
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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52 fourierspacing = 0.12
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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53 pme_order = 6
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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54 ewald_rtol = 1e-06
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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55 epsilon_surface = 0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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56 tcoupl = no
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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57 pcoupl = no
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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58 ld-seed = -1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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59 gen-seed = $seed
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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60 free_energy = no
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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61 delta_lambda = 0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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62 calc_lambda_neighbors = 1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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63 init-lambda-state = %L%
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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64
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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65 #if $path.select_path == "global":
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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66 fep-lambdas = $path.fep
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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67 #end if
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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68
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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69 #if $path.select_path in ["default1", "default2"]:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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70 coul-lambdas = $path.coul
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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71 vdw-lambdas = $path.vdw
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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72 bonded-lambdas = $path.bonded
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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73 #end if
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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74
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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75 sc-alpha = 0.5
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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76 sc-coul = no
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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77 sc-power = 1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
78 sc-sigma = 0.3
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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79 nstdhdl = 10
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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80
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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81 gen_vel = no
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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82 constraints = none
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
83 </configfile>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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84 <configfile name="nvt">
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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85 integrator = sd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
86 tinit = 0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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87 dt = $dt
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
88 nsteps = $nvtstep
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
89 nstcomm = 100
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
90 nstxout = 500
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
91 nstvout = 500
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
92 nstfout = 0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
93 nstlog = 500
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
94 nstenergy = 500
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
95 nstxout-compressed = 0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
96 cutoff-scheme = verlet
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
97 nstlist = 20
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
98 ns_type = grid
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
99 pbc = xyz
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
100 rlist = 1.2
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
101 coulombtype = PME
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
102 rcoulomb = 1.2
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
103 vdwtype = cutoff
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
104 vdw-modifier = potential-switch
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
105 rvdw-switch = 1.0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
106 rvdw = 1.2
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
107 DispCorr = EnerPres
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
108 fourierspacing = 0.12
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
109 pme_order = 6
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
110 ewald_rtol = 1e-06
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
111 epsilon_surface = 0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
112 tc_grps = system
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
113 tau_t = 1.0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
114 ref_t = $temperature
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
115 Pcoupl = No
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
116 tau_p = 0.5
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
117 compressibility = 4.5e-05
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
118 ref_p = $pressure
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
119 ld-seed = -1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
120 gen-seed = $seed
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
121 free_energy = no
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
122 delta_lambda = 0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
123 calc_lambda_neighbors = 1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
124 init-lambda-state = %L%
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
125
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
126 #if $path.select_path == "global":
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
127 fep-lambdas = $path.fep
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
128 #end if
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
129
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
130 #if $path.select_path in ["default1", "default2"]:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
131 coul-lambdas = $path.coul
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
132 vdw-lambdas = $path.vdw
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
133 bonded-lambdas = $path.bonded
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
134 #end if
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
135
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
136 sc-alpha = 0.5
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
137 sc-coul = no
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
138 sc-power = 1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
139 sc-sigma = 0.3
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
140 nstdhdl = 10
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
141 gen_vel = yes
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
142 gen_temp = 300
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
143
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
144 #if $constraints.cons == "no":
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
145 constraints = none
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
146 #end if
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
147
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
148 #if $constraints.cons == "yes":
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
149 constraints = $constraints.cons_type
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
150 constraint-algorithm = lincs
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
151 lincs-order = $constraints.lincs_order
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
152 lincs-iter = $constraints.lincs_iter
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
153 lincs-warnangle = $constraints.lincs_warnangle
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
154 #end if
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
155 </configfile>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
156 <configfile name="npt">
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
157 integrator = sd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
158 tinit = 0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
159 dt = $dt
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
160 nsteps = $nptstep
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
161 nstcomm = 100
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
162 nstxout = 500
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
163 nstvout = 500
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
164 nstfout = 0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
165 nstlog = 500
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
166 nstenergy = 500
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
167 nstxout-compressed = 0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
168 cutoff-scheme = verlet
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
169 nstlist = 20
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
170 ns_type = grid
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
171 pbc = xyz
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
172 rlist = 1.2
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
173 coulombtype = PME
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
174 rcoulomb = 1.2
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
175 vdwtype = cutoff
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
176 vdw-modifier = potential-switch
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
177 rvdw-switch = 1.0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
178 rvdw = 1.2
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
179 DispCorr = EnerPres
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
180 fourierspacing = 0.12
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
181 pme_order = 6
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
182 ewald_rtol = 1e-06
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
183 epsilon_surface = 0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
184 tc_grps = System
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
185 tau_t = 1.0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
186 ref_t = $temperature
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
187 Pcoupl = Berendsen
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
188 tau_p = 0.5
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
189 compressibility = 4.5e-05
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
190 ref_p = $pressure
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
191 ld-seed = -1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
192 gen-seed = $seed
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
193 free_energy = no
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
194 delta_lambda = 0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
195 calc_lambda_neighbors = 1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
196 init-lambda-state = %L%
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
197
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
198 #if $path.select_path == "global":
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
199 fep-lambdas = $path.fep
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
200 #end if
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
201
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
202 #if $path.select_path in ["default1", "default2"]:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
203 coul-lambdas = $path.coul
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
204 vdw-lambdas = $path.vdw
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
205 bonded-lambdas = $path.bonded
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
206 #end if
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
207
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
208 ; Options for the decoupling
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
209 sc-alpha = 0.5
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
210 sc-coul = no
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
211 sc-power = 1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
212 sc-sigma = 0.3
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
213 nstdhdl = 10
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
214 gen_vel = no
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
215
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
216 #if $constraints.cons == "no":
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
217 constraints = none
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
218 #end if
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
219
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
220 #if $constraints.cons == "yes":
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
221 constraints = $constraints.cons_type
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
222 constraint-algorithm = lincs
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
223 lincs-order = $constraints.lincs_order
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
224 lincs-iter = $constraints.lincs_iter
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
225 lincs-warnangle = $constraints.lincs_warnangle
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
226 #end if
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
227 </configfile>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
228 <configfile name="md">
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
229 integrator = sd
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
230 bd-fric = 0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
231 dt = $dt
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
232 nsteps = $mdstep
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
233 nstcomm = 100
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
234
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
235 nstxout = 10000
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
236 nstvout = 0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
237 nstfout = 0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
238 nstlog = 10000
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
239 nstenergy = 10000
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
240 nstxout-compressed = 0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
241
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
242 tcoupl = no
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
243 nsttcouple = 10
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
244 tc_grps = System
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
245 tau_t = 1.0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
246 ref_t = $temperature
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
247
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
248 #if $constraints.cons == "no":
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
249 constraints = none
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
250 #end if
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
251
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
252 #if $constraints.cons == "yes":
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
253 constraints = $constraints.cons_type
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
254 constraint-algorithm = lincs
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
255 lincs-order = $constraints.lincs_order
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
256 lincs-iter = $constraints.lincs_iter
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
257 lincs-warnangle = $constraints.lincs_warnangle
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
258 #end if
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
259
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
260 comm-mode = Linear
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
261
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
262 cutoff-scheme = Verlet
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
263 nstlist = 10
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
264 ns_type = grid
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
265 pbc = xyz
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
266 rlist = 0.8
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
267
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
268 coulombtype = PME
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
269 coulomb-modifier = none
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
270 rcoulomb = 0.8
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
271 fourierspacing = 0.10
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
272 pme_order = 4
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
273 ewald_rtol = 1.0E-5
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
274
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
275 vdwtype = cut-off
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
276 vdw-modifier = none
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
277 rvdw = 0.8
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
278 DispCorr = AllEnerPres
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
279
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
280 pcoupl = Parrinello-Rahman
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
281 pcoupltype = isotropic
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
282 tau_p = 2
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
283 compressibility = 4.5e-5
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
284 ref_p = $pressure
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
285 refcoord-scaling = com
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
286
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
287 gen-vel = no
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
288 continuation = yes
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
289
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
290 ld-seed = -1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
291 gen-seed = $seed
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
292
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
293 free-energy = yes
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
294 delta-lambda = 0 ; do not use slow growth method
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
295 init-lambda-state = %L%
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
296
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
297 #if $path.select_path == "global":
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
298 fep-lambdas = $path.fep
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
299 #end if
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
300
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
301 #if $path.select_path in ["default1", "default2"]:
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
302 coul-lambdas = $path.coul
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
303 vdw-lambdas = $path.vdw
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
304 bonded-lambdas = $path.bonded
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
305 #end if
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
306
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
307 nstdhdl = 10
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
308 nstcalcenergy = 10
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
309 calc-lambda-neighbors = -1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
310
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
311 #if $feoptions.feop == "default":
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
312 sc-alpha = 0.5
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
313 sc-coul = no
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
314 sc-power = 1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
315 sc-r-power = 6
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
316 sc-sigma = 0.3
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
317 couple-lambda0 = vdw-q
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
318 couple-lambda1 = none
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
319 couple-intramol = no
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
320 #end if
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
321
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
322 #if $feoptions.feop == "modify":
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
323 sc-alpha = $feoptions.scalpha
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
324 sc-coul = $feoptions.sccoul
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
325 sc-power = $feoptions.scpower
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
326 sc-r-power = $feoptions.scrpower
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
327 sc-sigma = $feoptions.scsigma
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
328 couple-lambda0 = $feoptions.couplelambda0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
329 couple-lambda1 = $feoptions.couplelambda1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
330 couple-intramol = $feoptions.coupleintramol
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
331 #end if
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
332
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
333 dhdl-derivatives = yes
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
334 dhdl-print-energy = no
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
335 separate-dhdl-file = yes
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
336 dh_hist_size = 0
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
337 dh_hist_spacing = 0.1
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
338
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
339 </configfile>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
340 </configfiles>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
341 <inputs>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
342 <param format="gro" name="groin" type="data" label="Structure (GRO) file" help="GRO input file with the merged structure."/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
343 <param format="top" name="topin" type="data" label="Topology (TOP) file" help="TOP input file with the merged structure."/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
344 <param name="minstep" type="integer" value="10000" label="Minimization steps" help="Number of steps for each free energy window."/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
345 <param name="nvtstep" type="integer" value="500000" label="NVT equilibration steps" help="Number of MD steps for NVT equilibration for each free energy window."/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
346 <param name="nptstep" type="integer" value="500000" label="NPT equilibration steps" help="Number of MD steps for NPT equilibration for each free energy window."/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
347 <param name="mdstep" type="integer" value="1000000" label="MD (production) steps" help="Number of MD steps for production runs of each free energy window."/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
348 <param name="seed" type="integer" value="19880924" label="Seed" help="Seed to initialize random generator for random velocities."/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
349 <param name="dt" type="float" value="0.001" label="Time step (ps)" help="Time step for integration."/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
350 <conditional name="constraints">
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
351 <param name="cons" type="select" label="Apply constraints to the ligands?" help="Constraints may be required to keep the ligands with alchemical states in the active site.">
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
352 <option value="yes">Yes</option>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
353 <option value="no">No</option>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
354 </param>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
355 <when value="no"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
356 <when value="yes">
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
357 <param name="cons_type" type="select" label="Constraints type" help="Convert all bonds to constraints, or only those containing hydrogen atoms">
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
358 <option value="h-bonds" selected="true">H-bonds</option>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
359 <option value="all-bonds">All bonds</option>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
360 </param>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
361 <param name="lincs_order" type="integer" value="4" label="LINCS order" help="Accuracy of LINCS algorithm. For normal MD simulations an order of 4 usually suffices, 6 is needed for large time-steps with virtual sites or BD."/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
362 <param name="lincs_iter" type="integer" value="1" label="LINCS iterations" help="Number of iterations to correct for rotational lengthening in LINCS. For normal runs a single step is sufficient."/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
363 <param name="lincs_warnangle" type="integer" value="30" label="LINCS maximum angle" help="Maximum angle that a bond can rotate before LINCS will complain / [deg]"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
364 </when>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
365 </conditional>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
366 <conditional name="path">
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
367 <param name="select_path" type="select" label="Select the FEP path">
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
368 <option value="global">Use global lambda scaling</option>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
369 <option value="default1">Default option 1 (change a larger ligand to a smaller ligand)</option>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
370 <option value="default2">Default option 2 (change a smaller ligand to a larger ligand)</option>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
371 </param>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
372 <when value="global">
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
373 <param name="lambda" type="text" value="2" label="Number of free energy windows"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
374 <param name="fep" type="text" value="0.00 0.50 1.00" label="FEP Lambdas" help="Global scaling - values must be between 0 and 1."/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
375 </when>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
376 <when value="default1">
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
377 <param name="lambda" type="text" value="40" label="Number of free energy windows"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
378 <param name="coul" type="text" value="0.00 0.11 0.22 0.33 0.44 0.56 0.67 0.78 0.89 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.000 1.00" label="Coulomb Lambdas (scaling electrostatics)" help="Values must be between 0 and 1."/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
379 <param name="vdw" type="text" value="0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00" label="Van der Waals Lambdas (scaling vdw interactions)" help="Values must be between 0 and 1."/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
380 <param name="bonded" type="text" value="0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00" label="Bonded Lambdas (scaling torsion)" help="Values must be between 0 and 1."/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
381 </when>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
382 <when value="default2">
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
383 <param name="lambda" type="text" value="40" label="Number of free energy windows"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
384 <param name="coul" type="text" value="0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.000 0.00 0.11 0.22 0.33 0.44 0.56 0.67 0.78 0.89 1.00 " label="Coulomb Lambdas (scaling electrostatics)" help="Values must be between 0 and 1."/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
385 <param name="vdw" type="text" value="0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00" label="Van der Waals Lambdas (scaling vdw interactions)" help="Values must be between 0 and 1."/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
386 <param name="bonded" type="text" value="0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00" label="Bonded Lambdas (scaling torsion)" help="Values must be between 0 and 1."/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
387 </when>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
388 </conditional>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
389 <conditional name="feoptions">
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
390 <param name="feop" type="select" label="Free energy variables">
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
391 <option value="default">Use default options</option>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
392 <option value="modify">Modify default options</option>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
393 </param>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
394 <when value="default"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
395 <when value="modify">
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
396 <param name="scalpha" type="float" value="0.5" label="The soft-core alpha parameter (sc-alpha)" />
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
397 <param name="scrpower" type="integer" value="6" label="The power of the radial term in the soft-core equation (sc-r-power)" />
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
398 <param name="scpower" type="integer" value="1" label="The power for lambda in the soft-core function (sc-power)" />
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
399 <param name="sccoul" type="text" value="no" label="Apply the soft-core free energy interaction transformation to the Columbic interaction of a molecule (sc-coul)? "/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
400 <param name="scsigma" type="float" value="0.3" label="The soft-core sigma" />
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
401 <param name="couplelambda0" type="text" value="vdw-q" label="Interactions at lambda=0" help="options are vdw-q, vdw, q, or none"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
402 <param name="couplelambda1" type="text" value="none" label="Interactions at lambda=1" help="options are vdw-q, vdw, q, or none"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
403 <param name="coupleintramol" type="text" value="no" label="Turn off intra-molecular interactions?" />
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
404 </when>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
405 </conditional>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
406 <param name="temperature" type="float" value="300.0" label="Temperature /K" />
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
407 <param name="pressure" type="float" value="1.0" label="Pressure /bar" />
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
408 <param name="input_fep" type="select" label="Perform simulation or only generate input files?">
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
409 <option value="perform">Perform simulation</option>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
410 <option value="generate">Only generate input files</option>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
411 </param>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
412 </inputs>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
413 <outputs>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
414 <data name="fepinpout" format="tar" from_work_dir="input_files.tar" label="Input files">
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
415 <filter>input_fep == 'generate'</filter>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
416 </data>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
417 <data name="dataout" format="tar" from_work_dir="data.tar" label="TI/FEP data output">
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
418 <filter>input_fep == 'perform'</filter>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
419 </data>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
420 <data name="trajout" format="tar" from_work_dir="traj.tar" label="Trajectories output">
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
421 <filter>input_fep == 'perform'</filter>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
422 </data>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
423 <data name="report" format="txt" label="Report">
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
424 <filter>input_fep == 'perform'</filter>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
425 </data>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
426 </outputs>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
427 <tests>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
428 <test>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
429 <param name="groin" value="morph.gro" ftype="gro"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
430 <param name="topin" value="morph.top" ftype="top"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
431 <param name="minstep" value="10"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
432 <param name="nvtstep" value="50"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
433 <param name="nptstep" value="50"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
434 <param name="mdstep" value="100"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
435 <param name="seed" value="19880924"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
436 <param name="cons" value="no"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
437 <param name="dt" value="0.001"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
438 <param name="path" value="global"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
439 <param name="lambda" value="2"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
440 <param name="fep" value="0.00 0.50 1.00"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
441 <param name="temperature" value="300.0"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
442 <param name="fepop" value="default"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
443 <param name="input_fep" value="perform"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
444 <param name="pressure" value="1.0"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
445 <output name="dataout" file="TI_FEP_data_output.tar" compare="sim_size"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
446 </test>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
447 <test>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
448 <param name="groin" value="morph.gro" ftype="gro"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
449 <param name="topin" value="morph.top" ftype="top"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
450 <param name="minstep" value="10000"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
451 <param name="nvtstep" value="500000"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
452 <param name="nptstep" value="500000"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
453 <param name="mdstep" value="1000000"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
454 <param name="seed" value="123546"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
455 <param name="cons" value="yes"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
456 <param name="cons_type" value="h-bonds"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
457 <param name="lincs_order" value="4"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
458 <param name="lincs_iter" value="1"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
459 <param name="incs_warnangle" value="30"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
460 <param name="dt" value="0.002"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
461 <param name="path" value="default2"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
462 <param name="lambda" value="40"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
463 <param name="coul" value="0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.000 0.00 0.11 0.22 0.33 0.44 0.56 0.67 0.78 0.89 1.00"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
464 <param name="vdw" value="0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
465 <param name="bonded" value="0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
466 <param name="temperature" value="300.0"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
467 <param name="fepop" value="default"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
468 <param name="input_fep" value="generate"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
469 <param name="pressure" value="1.0"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
470 <output name="fepinpout" file="Input_files.tar" compare="sim_size"/>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
471 </test>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
472 </tests>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
473 <help><![CDATA[
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
474 .. class:: infomark
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
475
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
476 **What it does**
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
477
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
478
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
479 - This tool can run the alchemical free energy calculations using GROMACS.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
480 - For more details about alchemical free energy calculations see http://www.alchemistry.org/wiki/Main_Page
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
481 - For details about GROMACS simulations see http://manual.gromacs.org/documentation/2019-rc1/user-guide/mdp-options.html
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
482
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
483 When you need to run the simulation outside Galaxy, you can generate and down load all the input files from this tool.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
484
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
485 1. Simply download the output "Input files".
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
486 2. Untar it using tar -xvf Galaxy3-\[Input_files\].tar
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
487 3. Run the bash script inside ./gmx_fep.sh {number of FEP windows}
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
488 - Give the number of FEP windows as an argument.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
489
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
490 This will generate input .MDP files and run all the steps for all the FEP windows iteratively.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
491
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
492
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
493 _____
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
494
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
495
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
496 .. class:: infomark
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
497
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
498 **Rules of Thumb for Intermediate States (taken from alchemistry.org)**
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
499
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
500 - These rules are not the end-all set and you should be familiar with why each one is suggested before just accepting them.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
501 - Bonded terms can be modified/turned off linearly. This includes angle or bond force constants as well as unconstrained bond distances.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
502 - Constrained bonds should not change length. There are free energy changes that cannot be ignored affiliated with this action.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
503 - Maximize similarity between states by removing/decoupling as few atoms as possible.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
504 - Do not open and close rings. This supersedes the previous rule.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
505 - Statistical uncertainty between any neighboring states should be equal. Rather challenging to do, but it has been proven to have the lowest variance path if you can pull it off.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
506 - Deleting or adding atoms should always be done with a soft core potential.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
507 - Changes in parameters can be done linearly.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
508 - All charge on atoms must be turned off prior to atomic repulsion. Otherwise you can get an infinite attractive potential and crash your simulation.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
509 - Similarly for only changes in terms, it's generally more efficient to change electrostatic terms separate from Lennard-Jones terms.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
510 - More states is better than fewer. Variance shrinks rapidly with number of states. You want the difference between intermediaries to be between 2-3 kBT
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
511
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
parents:
diff changeset
512 Obviously you will be limited on CPU power. Fewer states also leads to more samples begin required from each state, so take this into account when deciding number of states as well.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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513 However, for MBAR and TI, it can be shown that spreading samples across multiple states does not significantly affect the uncertainty, since for TI, each state contributes less to
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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514 the total uncertainty, and in MBAR, data contributes to the statistical precision of states with similar values of lambda.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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515
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
516 Shape of the variance does not significantly change with number of atoms, only magnitude. More intermediates will still be required for a large number of atoms to reduce statistical noise.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
517 Charge should be maintained across all λ
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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518
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
519 Simply having charged molecules is fine, but the net of the system should remain constant. If you must change the net charge, there are complicated ways to do so.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
520
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
521 Short prototype simulations are recommended. Even as short as 100 ps, the prototypes can provide rough magnitude of variance estimates,
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
522 although will likely under-predict the free energy as many configurations remain unsampled.
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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523
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
524
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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525 _____
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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526
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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527
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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528 .. class:: infomark
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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529
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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530 **Input**
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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531
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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532 - .GRO input
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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533 - .TOP input
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
534
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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535 _____
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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536
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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537
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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538 .. class:: infomark
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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539
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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540 **Output**
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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541
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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542 - TI/FEP data
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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543 - TI/FEP trajectory
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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544 - Report
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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545
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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546 ]]></help>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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547 <citations>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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548 <citation type="doi">10.1016/j.softx.2015.06.001</citation>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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549 <citation type="bibtex">@misc{alchemistrywiki, title={Alchemistry.org}, url={http://www.alchemistry.org/wiki/Main_Page}, journal={AlchemistryWiki}}
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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550 </citation>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
chemteam
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diff changeset
551 </citations>
19d1d4c30402 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
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552 </tool>