gmx_sim: sim.xml annotate

annotate sim.xml @ 21:c0c9a5024177 draft default tip

planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1

author	chemteam
date	Mon, 24 Oct 2022 22:35:05 +0000
parents	633f27174e8f
children

rev	line source
9 a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	1 <tool id="gmx_sim" name="GROMACS simulation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	2 <description>for system equilibration or data collection</description>
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	3 <macros>
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	4 <import>macros.xml</import>
18 633f27174e8f "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 7120a24dbb365d0a06595018a3b6f27dad0961e0" chemteam parents: 15 diff changeset	5 <token name="@GALAXY_VERSION@">0</token>
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	6 </macros>
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	7 <expand macro="requirements" />
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	8 <command detect_errors="exit_code"><![CDATA[
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	9 #if $sets.mdp.mdpfile == "custom":
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	10 ln -s '$sets.mdp.mdp_input' ./md.mdp &&
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	11 #end if
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	12 #if $sets.mdp.mdpfile == "default":
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	13 ln -s '$md' ./md.mdp &&
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	14 #end if
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	15
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	16 ln -s '$gro_input' ./inp.gro &&
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	17 ln -s '$top_input' ./top_input.top &&
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	18
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	19 #if $inps.itp_in:
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	20 ln -s '$inps.itp_in' ./posres.itp &&
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	21 #end if
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	22
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	23 #if $inps.cpt_in:
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	24 ln -s '$inps.cpt_in' ./inp.cpt &&
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	25 #end if
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	26
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	27 #if $inps.ndx_in:
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	28 ln -s '$inps.ndx_in' ./index.ndx &&
1 ec3f665cca3e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 10f45d117e34624bceb32442742ae0b8eb2dae30" chemteam parents: 0 diff changeset	29 #end if
ec3f665cca3e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 10f45d117e34624bceb32442742ae0b8eb2dae30" chemteam parents: 0 diff changeset	30
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	31 gmx grompp
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	32 -f ./md.mdp
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	33 -c ./inp.gro
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	34 #if $inps.cpt_in:
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	35 -t ./inp.cpt
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	36 #end if
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	37 #if $inps.itp_in:
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	38 -r ./inp.gro
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	39 #end if
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	40 #if $inps.ndx_in:
1 ec3f665cca3e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 10f45d117e34624bceb32442742ae0b8eb2dae30" chemteam parents: 0 diff changeset	41 -n ./index.ndx
ec3f665cca3e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 10f45d117e34624bceb32442742ae0b8eb2dae30" chemteam parents: 0 diff changeset	42 #end if
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	43 -p ./top_input.top
14 525ca7c8065f "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit bf18581ac3de6b65bdc0a988e6f844cea6e77975" chemteam parents: 13 diff changeset	44 -o outp.tpr @MAXWARN_CMD@ &>> verbose.txt &&
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	45
11 807aa4c9293d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit ab7232ec03a3361f808f5a0be0828e0f7fbd376d" chemteam parents: 10 diff changeset	46 #if "\${GPU_AVAILABLE:-0}" == 1:
807aa4c9293d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit ab7232ec03a3361f808f5a0be0828e0f7fbd376d" chemteam parents: 10 diff changeset	47 gmx_gpu mdrun
9 a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	48 -ntmpi 1
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	49 -nb gpu
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	50 -pme gpu
11 807aa4c9293d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit ab7232ec03a3361f808f5a0be0828e0f7fbd376d" chemteam parents: 10 diff changeset	51 #else:
807aa4c9293d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit ab7232ec03a3361f808f5a0be0828e0f7fbd376d" chemteam parents: 10 diff changeset	52 gmx mdrun
807aa4c9293d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit ab7232ec03a3361f808f5a0be0828e0f7fbd376d" chemteam parents: 10 diff changeset	53 #end if
807aa4c9293d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit ab7232ec03a3361f808f5a0be0828e0f7fbd376d" chemteam parents: 10 diff changeset	54 -nt "\${GALAXY_SLOTS:-4}"
9 a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	55 -deffnm outp &>> verbose.txt
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	56
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	57 #if $outps.str == 'pdb' or $outps.str == 'both'
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	58 && gmx editconf -f outp.gro -o outp.pdb &>> verbose.txt
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	59 #end if
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	60
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	61 && cat md.mdp &>> verbose.txt
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	62
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	63 ]]></command>
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	64 <configfiles>
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	65 <!-- .mdp file for the gromacs simulation -->
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	66 <configfile name="md">
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	67 #if $sets.mdp.mdpfile == 'default':
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	68 title = OPLS Lysozyme MD simulation
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	69 ; Run parameters
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	70 integrator = $sets.mdp.integrator ; leap-frog integrator
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	71 nsteps = $sets.mdp.md_steps ; 2 * 500000 = 1000 ps (1 ns)
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	72 dt = $sets.mdp.step_length ; 2 fs
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	73 ; Output control
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	74 nstxout = $sets.mdp.write_freq ; save coordinates every 10.0 ps
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	75 nstvout = $sets.mdp.write_freq ; save velocities every 10.0 ps
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	76 nstenergy = $sets.mdp.write_freq ; save energies every 10.0 ps
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	77 nstlog = $sets.mdp.write_freq ; update log file every 10.0 ps
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	78 nstxout-compressed = $sets.mdp.write_freq ; save compressed coordinates every 10.0 ps
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	79 ; nstxout-compressed replaces nstxtcout
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	80 compressed-x-grps = System ; group(s) to write to the compressed trajectory file
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	81 ; Bond parameters
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	82 #if $inps.cpt_in:
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	83 continuation = yes ; Restarting after NPT
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	84 #end if
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	85 constraint_algorithm = lincs ; holonomic constraints
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	86 constraints = $sets.mdp.constraints ; all bonds (even heavy atom-H bonds) constrained
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	87 lincs_iter = 1 ; accuracy of LINCS
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	88 lincs_order = 4 ; also related to accuracy
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	89 ; Neighborsearching
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	90 cutoff-scheme = $sets.mdp.cutoffscheme
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	91 ns_type = grid ; search neighboring grid cells
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	92 nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	93 rcoulomb = $sets.mdp.rcoulomb ; Short-range electrostatic cut-off
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	94 rlist = $sets.mdp.rlist ; Cut-off distance for the short-range neighbor list.
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	95 rvdw = $sets.mdp.rvdw ; Short-range Van der Waals cut-off
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	96 ; Electrostatics
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	97 coulombtype = $sets.mdp.coulombtype ; method for electrostatics calculations e.g. PME
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	98 pme_order = 4 ; cubic interpolation
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	99 fourierspacing = 0.16 ; grid spacing for FFT
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	100 ; Temperature coupling is on
15 ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	101 tcoupl = V-rescale ; modified Berendsen thermostat
ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	102 #if $sets.mdp.systemTcouple == "true":
ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	103 tc-grps = System ; coupling the whole system. Can be used in any system, beyond peptides.
ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	104 tau_t = 0.1 ; time constant in ps
ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	105 ref_t = $sets.mdp.temperature
ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	106 #else
ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	107 tc-grps = Protein Non-Protein ; two coupling groups - more accurate
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	108 tau_t = 0.1 0.1 ; time constant, in ps
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	109 ref_t = $sets.mdp.temperature $sets.mdp.temperature ; reference temperature, one for each group, in K
15 ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	110 #end if
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	111 ; Periodic boundary conditions
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	112 pbc = xyz ; 3-D PBC
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	113 ; Dispersion correction
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	114 DispCorr = EnerPres ; account for cut-off vdW scheme
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	115 ; Velocity generation
15 ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	116 #if $sets.ensembleselect.ensemble == "npt" or $sets.ensembleselect.startvel == "false":
ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	117 gen_vel = no ; Velocity generation is OFF
ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	118 #else
ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	119 gen_vel = yes ; Velocity generation is ON
ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	120 #end if
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	121 #end if
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	122 #if $inps.itp_in:
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	123 define = -DPOSRES ; position restrain the protein
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	124 refcoord_scaling = com
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	125 #end if
15 ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	126 #if $sets.ensembleselect.ensemble == "nvt":
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	127 pcoupl = no ; no pressure coupling in NVT
15 ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	128 #else:
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	129 ; Pressure coupling is on
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	130 pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	131 pcoupltype = isotropic ; uniform scaling of box vectors
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	132 tau_p = 2.0 ; time constant, in ps
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	133 ref_p = 1.0 ; reference pressure, in bar
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	134 compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	135 #end if
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	136
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	137 </configfile>
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	138
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	139 </configfiles>
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	140 <inputs>
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	141 <param argument="gro_input" type="data" format='gro' label="GRO structure file"/>
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	142 <param argument="top_input" type="data" format='top' label="Topology (TOP) file"/>
15 ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	143
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	144 <section name="inps" title="Inputs" expanded="false">
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	145
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	146 <!-- CPT inp -->
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	147 <!-- <conditional name="cpt_inp">
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	148 <param name="cpt_bool" type="select" label="Use a checkpoint (CPT) file" help="CPT file from a previous MD run">
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	149 <option value="yes">Continue simulation from a CPT file</option>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	150 <option value="no" selected="true">No CPT input</option>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	151 </param>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	152 <when value="yes">
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	153 <param argument="cpt_in" type="data" format='cpt' label="Checkpoint file"/>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	154 </when>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	155 <when value="no"/>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	156 </conditional> -->
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	157
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	158 <param argument="cpt_in" type="data" format='cpt' label="Checkpoint (CPT) file" optional="true" help="CPT file from a previous MD run. Leave empty if no checkpoint should be used."/>
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	159
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	160 <!-- ITP inp -->
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	161 <!-- <conditional name="posres">
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	162 <param name="posres_bool" type="select" label="Apply position restraints" help="Used e.g. for equilibration of solvent around a protein" value="false">
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	163 <option value="true">Apply position restraints</option>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	164 <option value="false" selected="true">No position restraints</option>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	165 </param>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	166 <when value="true">
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	167 <param argument="itp_in" type="data" format='itp' label="Position restraint (ITP) file"/>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	168 </when>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	169 <when value="false"/>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	170 </conditional> -->
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	171
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	172 <param argument="itp_in" type="data" format='itp' label="Position restraint (ITP) file" optional="true" help="Apply position restraints using a ITP file. Leave empty if no position restraints should be used."/>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	173
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	174 <!-- NDX inp -->
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	175 <!-- <conditional name="ndx_inp">
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	176 <param name="ndx_bool" type="select" label="Use a custom index (ndx) file" help="Use an index file specifying custom atom groups.">
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	177 <option value="true">Use custom index file</option>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	178 <option value="false" selected="true">Use default generated group</option>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	179 </param>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	180 <when value="true">
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	181 <param argument="ndx_in" type="data" format='ndx' label="Index file"/>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	182 </when>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	183 <when value="false"/>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	184 </conditional> -->
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	185
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	186 <param argument="ndx_in" type="data" format='ndx' label="Index (ndx) file" optional="true" help="Use an index file specifying custom atom groups. Leave empty to use default generated group"/>
15 ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	187
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	188
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	189 </section>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	190
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	191 <section name="outps" title="Outputs" expanded="false">
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	192 <!-- TRAJ out -->
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	193 <param argument="traj" type="select" label="Trajectory output">
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	194 <option value='none'>Return no trajectory output</option>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	195 <option value='xtc'>Return .xtc file (reduced precision)</option>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	196 <option value='trr'>Return .trr file (full precision)</option>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	197 <option value='both'>Return both .xtc and .trr files</option>
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	198 </param>
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	199
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	200 <!-- STR out -->
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	201 <param argument="str" type="select" label="Structure output">
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	202 <option value='none'>Return no structure output</option>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	203 <option value='gro'>Return .gro file</option>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	204 <option value='pdb'>Return .pdb file</option>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	205 <option value='both'>Return both .gro and .pdb files</option>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	206 </param>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	207
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	208 <!-- CPT out -->
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	209 <param name="cpt_out" type="select" label="Produce a checkpoint (CPT) file" help="Produce CPT file for a subsequent MD run">
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	210 <option value="true">Produce CPT output</option>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	211 <option value="false" selected="true">No CPT output</option>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	212 </param>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	213
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	214 <!-- EDR out -->
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	215 <param name="edr_out" type="select" label="Produce an energy (EDR) file" help="Produce file containing energies associated with the simulation">
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	216 <option value="true">Produce EDR output</option>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	217 <option value="false" selected="true">No EDR output</option>
1 ec3f665cca3e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 10f45d117e34624bceb32442742ae0b8eb2dae30" chemteam parents: 0 diff changeset	218 </param>
ec3f665cca3e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 10f45d117e34624bceb32442742ae0b8eb2dae30" chemteam parents: 0 diff changeset	219
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	220 <!-- XVG out -->
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	221 <param name="xvg_out" type="select" label="Produce XVG output" help="Produce tabular XVG file (e.g. forces from pulling simulations)" >
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	222 <option value="true">Produce XVG output</option>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	223 <option value="false" selected="true">No XVG output</option>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	224 </param>
4 cdaed42b4223 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1" chemteam parents: 3 diff changeset	225
cdaed42b4223 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1" chemteam parents: 3 diff changeset	226 <!-- TPR out -->
cdaed42b4223 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1" chemteam parents: 3 diff changeset	227 <param name="tpr_out" type="select" label="Produce TPR output" help="Produce TPR binary file" >
cdaed42b4223 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1" chemteam parents: 3 diff changeset	228 <option value="true">Produce TPR output</option>
cdaed42b4223 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1" chemteam parents: 3 diff changeset	229 <option value="false" selected="true">No TPR output</option>
cdaed42b4223 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1" chemteam parents: 3 diff changeset	230 </param>
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	231
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	232 </section>
1 ec3f665cca3e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 10f45d117e34624bceb32442742ae0b8eb2dae30" chemteam parents: 0 diff changeset	233
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	234 <section name="sets" title="Settings" expanded="false">
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	235 <!-- other ... -->
15 ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	236
ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	237 <conditional name="ensembleselect">
ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	238 <param name="ensemble" label="Ensemble" type="select" help="NVT ensemble (constant number of particles, volume and temperature) or NPT ensemble (constant number of particles, pressure and temperature)">
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	239 <option value="nvt">Isothermal-isochoric ensemble (NVT)</option>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	240 <option value="npt">Isothermal-isobaric ensemble (NPT)</option>
15 ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	241 </param>
ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	242 <when value="nvt">
ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	243 <param argument="startvel" type="select" label="Starting Velocities">
ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	244 <option value="true">Assign starting velocities (recommended for NVT)</option>
ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	245 <option value="false" selected="true">Do not assign starting velocities</option>
ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	246 </param>
ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	247 </when>
ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	248 <when value="npt" />
ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	249 </conditional>
ea0e6d2f1be7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0" chemteam parents: 14 diff changeset	250 <expand macro="md_inputs"/>
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	251 </section>
14 525ca7c8065f "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit bf18581ac3de6b65bdc0a988e6f844cea6e77975" chemteam parents: 13 diff changeset	252
525ca7c8065f "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit bf18581ac3de6b65bdc0a988e6f844cea6e77975" chemteam parents: 13 diff changeset	253 <expand macro="maxwarn" />
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	254 <expand macro="log" />
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	255
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	256 </inputs>
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	257 <outputs>
13 da8753545526 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3" chemteam parents: 12 diff changeset	258 <data name="output1" format="gro" from_work_dir="outp.gro" label="GROMACS simulation (GRO) on ${on_string}">
4 cdaed42b4223 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1" chemteam parents: 3 diff changeset	259 <filter>outps["str"] == 'gro' or outps["str"] == 'both'</filter>
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	260 </data>
13 da8753545526 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3" chemteam parents: 12 diff changeset	261 <data name="output2" format="pdb" from_work_dir="outp.pdb" label="GROMACS simulation (PDB) file on ${on_string}">
4 cdaed42b4223 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1" chemteam parents: 3 diff changeset	262 <filter>outps["str"] == 'pdb' or outps["str"] == 'both'</filter>
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	263 </data>
13 da8753545526 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3" chemteam parents: 12 diff changeset	264 <data name="output3" format="trr" from_work_dir="outp.trr" label="GROMACS simulation (TRR) on ${on_string}">
4 cdaed42b4223 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1" chemteam parents: 3 diff changeset	265 <filter>outps["traj"] == 'trr' or outps["traj"] == 'both'</filter>
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	266 </data>
13 da8753545526 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3" chemteam parents: 12 diff changeset	267 <data name="output4" format="xtc" from_work_dir="outp.xtc" label="GROMACS simulation (XTC) on ${on_string}">
4 cdaed42b4223 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1" chemteam parents: 3 diff changeset	268 <filter>outps["traj"] == 'xtc' or outps["traj"] == 'both'</filter>
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	269 </data>
13 da8753545526 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3" chemteam parents: 12 diff changeset	270 <data name="output5" format="cpt" from_work_dir="outp.cpt" label="GROMACS simulation (CPT) on ${on_string}">
4 cdaed42b4223 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1" chemteam parents: 3 diff changeset	271 <filter>outps["cpt_out"] == 'true'</filter>
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	272 </data>
13 da8753545526 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3" chemteam parents: 12 diff changeset	273 <data name="output6" format="edr" from_work_dir="outp.edr" label="GROMACS simulation (EDR) on ${on_string}">
4 cdaed42b4223 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1" chemteam parents: 3 diff changeset	274 <filter>outps["edr_out"] == 'true'</filter>
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	275 </data>
13 da8753545526 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3" chemteam parents: 12 diff changeset	276 <data name="output7" format="xvg" from_work_dir="outp_pullf.xvg" label="GROMACS simulation (XVG) on ${on_string}">
5 171ce1253b19 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3786d1760d039118fa87c5df52d59eec0a5781a3" chemteam parents: 4 diff changeset	277 <filter>outps["xvg_out"] == 'true'</filter>
171ce1253b19 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3786d1760d039118fa87c5df52d59eec0a5781a3" chemteam parents: 4 diff changeset	278 </data>
12 73008ef1f487 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1bf804ff637b03d2c4b6c8a9ff1cc5dfd53d1c0b" chemteam parents: 11 diff changeset	279 <data name="output7_1" format="xvg" from_work_dir="outp.xvg">
73008ef1f487 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1bf804ff637b03d2c4b6c8a9ff1cc5dfd53d1c0b" chemteam parents: 11 diff changeset	280 <filter>outps["xvg_out"] == 'true'</filter>
73008ef1f487 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1bf804ff637b03d2c4b6c8a9ff1cc5dfd53d1c0b" chemteam parents: 11 diff changeset	281 </data>
5 171ce1253b19 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3786d1760d039118fa87c5df52d59eec0a5781a3" chemteam parents: 4 diff changeset	282 <!-- <collection name="output7" type="list">
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	283 <discover_datasets pattern="(?P<designation>.*)\.xvg" visible="true" directory="." />
4 cdaed42b4223 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1" chemteam parents: 3 diff changeset	284 <filter>outps["xvg_out"] == 'true'</filter>
5 171ce1253b19 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3786d1760d039118fa87c5df52d59eec0a5781a3" chemteam parents: 4 diff changeset	285 </collection> -->
13 da8753545526 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3" chemteam parents: 12 diff changeset	286 <data name="output8" format="tpr" from_work_dir="outp.tpr">
4 cdaed42b4223 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1" chemteam parents: 3 diff changeset	287 <filter>outps["tpr_out"] == 'true'</filter>
cdaed42b4223 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1" chemteam parents: 3 diff changeset	288 </data>
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	289
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	290 <expand macro="log_outputs" />
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	291 </outputs>
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	292
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	293 <tests>
4 cdaed42b4223 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1" chemteam parents: 3 diff changeset	294 <test expect_num_outputs="3">
9 a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	295 <param name="gro_input" value="str_ions.gro" />
13 da8753545526 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3" chemteam parents: 12 diff changeset	296 <param name="top_input" value="topol_md.top" />
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	297 <!-- <param name="cpt_bool" value="yes" /> -->
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	298 <param name="cpt_in" value="npt.cpt" />
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	299 <param name="mdpfile" value="custom" />
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	300 <param name="mdp_input" value="md.mdp" />
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	301 <!-- <param name="ndx_bool" value="false" /> -->
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	302 <param name="traj" value="trr"/>
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	303 <param name="str" value="gro"/>
4 cdaed42b4223 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1" chemteam parents: 3 diff changeset	304 <param name="tpr_out" value="true"/>
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	305 <param name="ensemble" value="npt" />
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	306 <!-- <param name="posres_bool" value="false" /> -->
9 a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	307 <output name="output1" ftype="gro">
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	308 <assert_contents>
9 a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	309 <has_size value="6537" />
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	310 <has_n_lines n="97" />
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	311 <has_line line="TEST in water" />
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	312 </assert_contents>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	313 </output>
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	314 <output name="output3" ftype="trr">
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	315 <assert_contents>
9 a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	316 <has_size value="26136" />
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	317 </assert_contents>
9 a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	318 </output>
13 da8753545526 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3" chemteam parents: 12 diff changeset	319 <output name="output8" ftype="tpr">
9 a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	320 <assert_contents>
18 633f27174e8f "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 7120a24dbb365d0a06595018a3b6f27dad0961e0" chemteam parents: 15 diff changeset	321 <has_size value="44400" />
9 a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	322 </assert_contents>
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	323 </output>
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	324 </test>
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	325
4 cdaed42b4223 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1" chemteam parents: 3 diff changeset	326 <test expect_num_outputs="3">
9 a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	327 <param name="gro_input" value="str_ions.gro" />
13 da8753545526 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3" chemteam parents: 12 diff changeset	328 <param name="top_input" value="topol_md.top" />
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	329 <!-- <param name="cpt_bool" value="yes" /> -->
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	330 <param name="cpt_in" value="npt.cpt" />
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	331 <!-- <param name="ndx_bool" value="false" /> -->
1 ec3f665cca3e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 10f45d117e34624bceb32442742ae0b8eb2dae30" chemteam parents: 0 diff changeset	332 <param name="traj" value="trr"/>
ec3f665cca3e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 10f45d117e34624bceb32442742ae0b8eb2dae30" chemteam parents: 0 diff changeset	333 <param name="str" value="both"/>
ec3f665cca3e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 10f45d117e34624bceb32442742ae0b8eb2dae30" chemteam parents: 0 diff changeset	334 <expand macro="test_params"/>
ec3f665cca3e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 10f45d117e34624bceb32442742ae0b8eb2dae30" chemteam parents: 0 diff changeset	335 <param name="ensemble" value="npt" />
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	336 <!-- <param name="posres_bool" value="false" /> -->
9 a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	337 <output name="output1" ftype="gro">
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	338 <assert_contents>
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	339 <has_size value="6537" />
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	340 <has_n_lines n="97" />
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	341 <has_line line="TEST in water" />
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	342 </assert_contents>
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	343 </output>
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	344 <output name="output2" ftype="pdb">
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	345 <assert_contents>
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	346 <has_size value="7582" />
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	347 <has_n_lines n="100" />
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	348 <has_line line="TITLE TEST in water" />
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	349 <has_line line="REMARK THIS IS A SIMULATION BOX" />
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	350 </assert_contents>
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	351 </output>
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	352 <output name="output3" ftype="trr">
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	353 <assert_contents>
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	354 <has_size value="26136" />
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	355 </assert_contents>
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	356 </output>
1 ec3f665cca3e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 10f45d117e34624bceb32442742ae0b8eb2dae30" chemteam parents: 0 diff changeset	357 </test>
ec3f665cca3e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 10f45d117e34624bceb32442742ae0b8eb2dae30" chemteam parents: 0 diff changeset	358
4 cdaed42b4223 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1" chemteam parents: 3 diff changeset	359 <test expect_num_outputs="3">
9 a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	360 <param name="gro_input" value="str_ions.gro" />
13 da8753545526 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3" chemteam parents: 12 diff changeset	361 <param name="top_input" value="topol_md.top" />
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	362 <!-- <param name="cpt_bool" value="yes" /> -->
1 ec3f665cca3e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 10f45d117e34624bceb32442742ae0b8eb2dae30" chemteam parents: 0 diff changeset	363 <param name="cpt_in" value="npt.cpt" />
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	364 <!-- <param name="ndx_bool" value="true" /> -->
1 ec3f665cca3e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 10f45d117e34624bceb32442742ae0b8eb2dae30" chemteam parents: 0 diff changeset	365 <param name="ndx_in" value="index.ndx" />
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	366 <param name="traj" value="trr"/>
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	367 <param name="str" value="both"/>
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	368 <expand macro="test_params"/>
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	369 <param name="ensemble" value="npt" />
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	370 <!-- <param name="posres_bool" value="false" /> -->
13 da8753545526 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3" chemteam parents: 12 diff changeset	371 <output name="output1" ftype="gro">
9 a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	372 <assert_contents>
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	373 <has_size value="6537" />
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	374 <has_n_lines n="97" />
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	375 </assert_contents>
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	376 </output>
13 da8753545526 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3" chemteam parents: 12 diff changeset	377 <output name="output2" ftype="pdb">
9 a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	378 <assert_contents>
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	379 <has_size value="7582" />
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	380 <has_n_lines n="100" />
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	381 <has_line line="TITLE TEST in water" />
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	382 <has_line line="REMARK THIS IS A SIMULATION BOX" />
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	383 </assert_contents>
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	384 </output>
13 da8753545526 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3" chemteam parents: 12 diff changeset	385 <output name="output3" ftype="trr">
9 a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	386 <assert_contents>
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	387 <has_size value="26136" />
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	388 </assert_contents>
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	389 </output>
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	390 </test>
4 cdaed42b4223 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1" chemteam parents: 3 diff changeset	391 <test expect_num_outputs="3">
9 a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	392 <param name="gro_input" value="str_ions.gro" />
13 da8753545526 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3" chemteam parents: 12 diff changeset	393 <param name="top_input" value="topol_md.top" />
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	394 <!-- <param name="posres_bool" value="true" /> -->
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	395 <param name="itp_in" value="posres.itp" />
5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	396 <!-- <param name="cpt_bool" value="no" /> -->
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	397 <param name="cpt_out" value="true" />
2 5642f48f5698 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" chemteam parents: 1 diff changeset	398 <!-- <param name="ndx_bool" value="false" /> -->
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	399 <param name="traj" value="xtc"/>
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	400 <param name="str" value="pdb"/>
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	401 <param name="ensemble" value="nvt" />
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	402 <expand macro="test_params"/>
13 da8753545526 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3" chemteam parents: 12 diff changeset	403
9 a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	404 <output name="output2" ftype="pdb">
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	405 <assert_contents>
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	406 <has_size value="7582" />
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	407 <has_n_lines n="100" />
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	408 <has_line line="TITLE TEST in water" />
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	409 <has_line line="REMARK THIS IS A SIMULATION BOX" />
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	410 </assert_contents>
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	411 </output>
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	412 <output name="output4" ftype="xtc">
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	413 <assert_contents>
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	414 <has_size value="4910" delta="20"/>
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	415 </assert_contents>
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	416 </output>
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	417 <output name="output5" ftype="cpt">
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	418 <assert_contents>
10 f197e34c33a9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc" chemteam parents: 9 diff changeset	419 <has_size value="3350" delta="100"/>
9 a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	420 </assert_contents>
a97dcfc23b4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b" chemteam parents: 5 diff changeset	421 </output>
0 1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	422 </test>
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	423 </tests>
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	424
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	425 <help><![CDATA[
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	426
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	427 .. class:: infomark
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	428
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	429 What it does
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	430
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	431 This tool performs a molecular dynamics simulation with GROMACS.
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	432
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	433 _____
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	434
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	435 .. class:: infomark
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	436
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	437 Input
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	438
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	439 - GRO structure file.
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	440 - Topology (TOP) file.
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	441
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	442 A variety of other options can also be specified:
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	443 - MDP parameter file to take advantage of all GROMACS features. Otherwise, choose parameters through the Galaxy interface. See the `manual`_ for more information on the options.
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	444 - Accepting and producing checkpoint (CPT) input/output files, which allows sequential MD simulations, e.g. when performing NVT and NPT equilibration followed by a production simulation.
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	445 - Position restraint (ITP) file, useful for equilibrating solvent around a protein.
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	446 - Choice of ensemble: NVT or NPT.
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	447 - Whether to return trajectory (XTC or TRR) and/or structure (GRO or PDB) files.
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	448
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	449 .. _`manual`: http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	450
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	451 _____
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	452
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	453
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	454 .. class:: infomark
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	455
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	456 Output
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	457
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	458 - Structure and/or trajectory files as specified in the input.
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	459
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	460 ]]></help>
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	461
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	462 <expand macro="citations" />
1a5960636405 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" chemteam parents: diff changeset	463 </tool>

Mercurial > repos > chemteam > gmx_sim

annotate sim.xml @ 21:c0c9a5024177 draft default tip