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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit b1b74e91a242f2de250761a79b17d77e68b1045f"
author chemteam
date Fri, 30 Aug 2019 15:07:22 -0400
parents 609d93596b61
children
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d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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1 <tool id="gmx_md" name="GROMACS production simulation" version="@VERSION@">
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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2 <description>for data collection</description>
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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3 <macros>
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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4 <import>macros.xml</import>
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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5 </macros>
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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6 <expand macro="requirements" />
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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7 <command detect_errors="exit_code"><![CDATA[
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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8 #if $mdp.mdpfile == "custom":
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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9 ln -s '$mdp.mdp_input' ./md.mdp &&
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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10 #end if
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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11 #if $mdp.mdpfile == "default":
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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12 ln -s '$md' ./md.mdp &&
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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13 #end if
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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14
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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15 ln -s '$gro_input' ./npt.gro &&
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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16 ln -s '$cpt_input' ./npt.cpt &&
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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17 ln -s '$top_input' ./top_input.top &&
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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18
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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19
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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20 gmx grompp -f ./md.mdp -c ./npt.gro -t ./npt.cpt -p ./top_input.top -o md_0_1.tpr &>> verbose.txt &&
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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21 gmx mdrun -deffnm md_0_1 &>> verbose.txt
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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22
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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23 #if $str == 'pdb' or $str == 'both'
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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24 && gmx editconf -f md_0_1.gro -o md_0_1.pdb &>> verbose.txt
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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25 #end if
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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26
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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27
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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28 ]]></command>
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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29 <configfiles>
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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30 <!-- .mdp file for the gromacs simulation -->
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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31 <configfile name="md">
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32 #if $mdp.mdpfile == 'default':
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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33 title = OPLS Lysozyme MD simulation
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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34 ; Run parameters
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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35 integrator = $mdp.integrator ; leap-frog integrator
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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36 nsteps = $mdp.md_steps ; 2 * 500000 = 1000 ps (1 ns)
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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37 dt = $mdp.step_length ; 2 fs
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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38 ; Output control
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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39 nstxout = $mdp.write_freq ; save coordinates every 10.0 ps
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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40 nstvout = $mdp.write_freq ; save velocities every 10.0 ps
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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41 nstenergy = $mdp.write_freq ; save energies every 10.0 ps
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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42 nstlog = $mdp.write_freq ; update log file every 10.0 ps
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43 nstxout-compressed = $mdp.write_freq ; save compressed coordinates every 10.0 ps
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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44 ; nstxout-compressed replaces nstxtcout
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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45 compressed-x-grps = System ; group(s) to write to the compressed trajectory file
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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46 ; Bond parameters
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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47 continuation = yes ; Restarting after NPT
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48 constraint_algorithm = lincs ; holonomic constraints
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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49 constraints = $mdp.constraints ; all bonds (even heavy atom-H bonds) constrained
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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50 lincs_iter = 1 ; accuracy of LINCS
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51 lincs_order = 4 ; also related to accuracy
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52 ; Neighborsearching
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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53 cutoff-scheme = $mdp.cutoffscheme
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54 ns_type = grid ; search neighboring grid cells
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55 nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
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56 rcoulomb = $mdp.rcoulomb ; Short-range electrostatic cut-off
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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57 rlist = $mdp.rlist ; Cut-off distance for the short-range neighbor list.
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58 rvdw = $mdp.rvdw ; Short-range Van der Waals cut-off
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59 ; Electrostatics
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60 coulombtype = $mdp.coulombtype ; method for electrostatics calculations e.g. PME
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61 pme_order = 4 ; cubic interpolation
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62 fourierspacing = 0.16 ; grid spacing for FFT
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63 ; Temperature coupling is on
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64 tcoupl = V-rescale ; modified Berendsen thermostat
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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65 tc-grps = Protein Non-Protein ; two coupling groups - more accurate
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66 tau_t = 0.1 0.1 ; time constant, in ps
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67 ref_t = $mdp.temperature $mdp.temperature ; reference temperature, one for each group, in K
d97433b7d482 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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68 ; Pressure coupling is on
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69 pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
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70 pcoupltype = isotropic ; uniform scaling of box vectors
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71 tau_p = 2.0 ; time constant, in ps
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72 ref_p = 1.0 ; reference pressure, in bar
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73 compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
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74 ; Periodic boundary conditions
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75 pbc = xyz ; 3-D PBC
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76 ; Dispersion correction
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77 DispCorr = EnerPres ; account for cut-off vdW scheme
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78 ; Velocity generation
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79 gen_vel = no ; Velocity generation is off
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80 #end if
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81 </configfile>
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82
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83 </configfiles>
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84 <inputs>
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85 <param argument="gro_input" type="data" format='gro' label="GRO structure file."/>
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86 <param argument="top_input" type="data" format='top' label="Topology (TOP) file."/>
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87 <param argument="cpt_input" type="data" format='cpt' label="Checkpoint (CPT) file from NVT run."/>
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88
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89 <expand macro="md_inputs"/>
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90 </inputs>
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91 <outputs>
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92 <data name="output1" format="gro" from_work_dir="md_0_1.gro">
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93 <filter>str == 'gro' or str == 'both'</filter>
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94 </data>
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95 <data name="output2" format="pdb" from_work_dir="md_0_1.pdb">
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96 <filter>str == 'pdb' or str == 'both'</filter>
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97 </data>
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98 <data name="output3" format="trr" from_work_dir="md_0_1.trr">
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99 <filter>traj == 'trr' or traj == 'both'</filter>
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100 </data>
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101 <data name="output4" format="xtc" from_work_dir="md_0_1.xtc">
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102 <filter>traj == 'xtc' or traj == 'both'</filter>
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103 </data>
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104
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105 <data name="report" format="txt" from_work_dir="verbose.txt">
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106 <filter>capture_log</filter>
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107 </data>
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108 </outputs>
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109 <tests>
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110 <test>
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111 <param name="gro_input" value="npt.gro" />
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112 <param name="top_input" value="topol_solv.top" />
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113 <param name="cpt_input" value="npt.cpt" />
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114 <param name="traj" value="trr"/>
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115 <param name="str" value="both"/>
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116
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117 <expand macro="test_params"/>
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118
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119 <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/>
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120 <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/>
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121 <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/>
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122 </test>
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123 <test>
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124 <param name="gro_input" value="npt.gro" />
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125 <param name="top_input" value="topol_solv.top" />
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126 <param name="cpt_input" value="npt.cpt" />
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127 <param name="itp_input" value="posres.itp" />
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128 <param name="traj" value="xtc"/>
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129 <param name="str" value="pdb"/>
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130
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131 <expand macro="test_params"/>
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132
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133 <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/>
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134 <output name="output4" file="md_0_1.xtc" ftype="xtc" compare="sim_size"/>
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135 </test>
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136 <test>
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137 <param name="gro_input" value="npt.gro" />
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138 <param name="top_input" value="topol_solv.top" />
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139 <param name="cpt_input" value="npt.cpt" />
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140 <param name="mdpfile" value="custom" />
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141 <param name="mdp_input" value="md.mdp" />
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142 <param name="traj" value="trr"/>
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143 <param name="str" value="gro"/>
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144 <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/>
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145 <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/>
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146 </test>
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147 </tests>
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148 <help><![CDATA[
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149
1
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150 Upload GRO and TOP files for the production simulation, as well as the checkpoint (CPT) file from the NPT equilibration. To take advantage of all GROMACS features, upload an MDP file with simulation parameters. Otherwise, choose parameters through the Galaxy interface. See http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html for more information on the options.
0
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151 ]]></help>
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152
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153 <expand macro="citations" />
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154 </tool>