annotate nvt.xml @ 2:d861e980340f draft default tip

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit b1b74e91a242f2de250761a79b17d77e68b1045f"
author chemteam
date Fri, 30 Aug 2019 15:05:30 -0400
parents 3a018cc1f690
children
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f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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1 <tool id="gmx_nvt" name="GROMACS NVT equilibration" version="@VERSION@">
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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2 <description>- constant-temperature and -volume equilibration of a system</description>
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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3 <macros>
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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4 <import>macros.xml</import>
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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5 </macros>
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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6
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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7 <expand macro="requirements" />
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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8
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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9 <command detect_errors="exit_code"><![CDATA[
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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10 #if $mdp.mdpfile == "custom":
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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11 ln -s '$mdp.mdp_input' ./nvt.mdp &&
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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12 #end if
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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13 #if $mdp.mdpfile == "default":
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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14 ln -s '$nvt' ./nvt.mdp &&
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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15 #end if
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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16
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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17 ln -s '$gro_input' ./em.gro &&
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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18 ln -s '$top_input' ./top_input.top &&
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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19 ln -s '$itp_input' ./posres.itp &&
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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20
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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21 gmx grompp -f ./nvt.mdp -c ./em.gro -r ./em.gro -p ./top_input.top -o nvt.tpr &>> verbose.txt &&
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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22 gmx mdrun -deffnm nvt &>> verbose.txt
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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23
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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24 #if $str == 'pdb' or $str == 'both'
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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25 && gmx editconf -f nvt.gro -o nvt.pdb &>> verbose.txt
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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26 #end if
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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27 ]]></command>
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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28 <configfiles>
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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29 <!-- .mdp file for the gromacs simulation -->
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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30 <configfile name="nvt">
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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31 #if $mdp.mdpfile == 'default':
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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32 title = NVT equilibration
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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33 define = -DPOSRES ; position restrain the protein
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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34 ; Run parameters
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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35 integrator = $mdp.integrator ; leap-frog integrator
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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36 nsteps = $mdp.md_steps ; 2 * 50000 = 100 ps
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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37 dt = $mdp.step_length ; 2 fs
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38 ; Output control
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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39 nstxout = $mdp.write_freq ; save coordinates every n ps
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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40 nstvout = $mdp.write_freq ; save velocities every n ps
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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41 nstenergy = $mdp.write_freq ; save energies every n ps
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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42 nstlog = $mdp.write_freq ; update log file every n ps
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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43 nstxout-compressed = $mdp.write_freq ; save compressed coordinates every 10.0 ps
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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44 ; Bond parameters
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45 continuation = no ; first dynamics run
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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46 constraint_algorithm = lincs ; holonomic constraints
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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47 constraints = $mdp.constraints ; all bonds (even heavy atom-H bonds) constrained
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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48 lincs_iter = 1 ; accuracy of LINCS
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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49 lincs_order = 4 ; also related to accuracy
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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50 ; Neighborsearching
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51 cutoff-scheme = $mdp.cutoffscheme
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52 ns_type = grid ; search neighboring grid cells
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53 nstlist = 10 ; 20 fs, largely irrelevant with Verlet
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54 rcoulomb = $mdp.rcoulomb ; Short-range electrostatic cut-off
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55 rlist = $mdp.rlist ; Cut-off distance for the short-range neighbor list.
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56 rvdw = $mdp.rvdw ; Short-range Van der Waals cut-off
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57 ; Electrostatics
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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58 coulombtype = $mdp.coulombtype ; method for electrostatics calculations e.g. PME
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59 pme_order = 4 ; cubic interpolation
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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60 fourierspacing = 0.16 ; grid spacing for FFT
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61 ; Temperature coupling is on
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62 tcoupl = V-rescale ; modified Berendsen thermostat
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63 tc-grps = Protein Non-Protein ; two coupling groups - more accurate
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64 tau_t = 0.1 0.1 ; time constant, in ps
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65 ref_t = $mdp.temperature $mdp.temperature ; reference temperature, one for each group, in K
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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66 ; Pressure coupling is off
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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67 pcoupl = no ; no pressure coupling in NVT
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68 ; Periodic boundary conditions
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69 pbc = xyz ; 3-D PBC
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70 ; Dispersion correction
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71 DispCorr = EnerPres ; account for cut-off vdW scheme
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72 ; Velocity generation
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73 gen_vel = yes ; assign velocities from Maxwell distribution
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74 gen_temp = 300 ; temperature for Maxwell distribution
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75 gen_seed = -1 ; generate a random seed
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76 #end if
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77 </configfile>
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78
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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79 </configfiles>
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80 <inputs>
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81 <param argument="gro_input" type="data" format='gro' label="GRO structure file."/>
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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82 <param argument="top_input" type="data" format='top' label="Topology (TOP) file."/>
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83 <param argument="itp_input" type="data" format='itp' label="Position restraint file."/>
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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84
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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85 <expand macro="md_inputs"/>
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86 </inputs>
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87 <outputs>
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88 <data name="output1" format="gro" from_work_dir="nvt.gro">
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89 <filter>str == 'gro' or str == 'both'</filter>
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90 </data>
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91 <data name="output5" format="pdb" from_work_dir="nvt.pdb">
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92 <filter>str == 'pdb' or str == 'both'</filter>
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93 </data>
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94 <data name="output2" format="cpt" from_work_dir="nvt.cpt"/>
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95 <data name="output3" format="trr" from_work_dir="nvt.trr">
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96 <filter>traj == 'trr' or traj == 'both'</filter>
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97 </data>
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98 <data name="output4" format="xtc" from_work_dir="nvt.xtc">
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99 <filter>traj == 'xtc' or traj == 'both'</filter>
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100 </data>
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101 <data name="report" format="txt" from_work_dir="verbose.txt">
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102 <filter>capture_log</filter>
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103 </data>
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104 </outputs>
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105 <tests>
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106 <test>
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107 <param name="gro_input" value="em.gro" />
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108 <param name="top_input" value="topol_solv.top" />
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109 <param name="itp_input" value="posres.itp" />
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110 <param name="traj" value="xtc"/>
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111 <param name="str" value="both"/>
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112
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113 <expand macro="test_params"/>
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114
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115 <output name="output1" file="nvt.gro" ftype="gro" compare="sim_size"/>
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116 <output name="output2" file="nvt.cpt" ftype="cpt" compare="sim_size"/>
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117 <output name="output4" file="nvt.xtc" ftype="xtc" compare="sim_size"/>
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118 <output name="output5" file="nvt.pdb" ftype="pdb" compare="sim_size"/>
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119
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120 </test>
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121 <test>
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122 <param name="gro_input" value="em.gro" />
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123 <param name="top_input" value="topol_solv.top" />
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124 <param name="itp_input" value="posres.itp" />
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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125 <param name="traj" value="xtc"/>
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126 <param name="str" value="pdb"/>
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127
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128 <expand macro="test_params"/>
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129
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130 <output name="output2" file="nvt.cpt" ftype="cpt" compare="sim_size"/>
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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131 <output name="output4" file="nvt.xtc" ftype="xtc" compare="sim_size"/>
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132 <output name="output5" file="nvt.pdb" ftype="pdb" compare="sim_size"/>
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133
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134 </test>
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135 <test>
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136 <param name="gro_input" value="em.gro" />
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137 <param name="top_input" value="topol_solv.top" />
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138 <param name="itp_input" value="posres.itp" />
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139 <param name="str" value="gro"/>
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140 <param name="traj" value="trr"/>
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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141
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142 <expand macro="test_params"/>
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143
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144 <output name="output1" file="nvt.gro" ftype="gro" compare="sim_size"/>
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145 <output name="output2" file="nvt.cpt" ftype="cpt" compare="sim_size"/>
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146 <output name="output3" file="nvt.trr" ftype="trr" compare="sim_size"/>
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147 </test>
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148 <test>
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149 <param name="gro_input" value="em.gro" />
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150 <param name="top_input" value="topol_solv.top" />
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151 <param name="itp_input" value="posres.itp" />
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152 <param name="mdpfile" value="custom" />
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153 <param name="mdp_input" value="nvt.mdp" />
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154 <param name="traj" value="none"/>
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155 <param name="str" value="gro"/>
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156 <output name="output1" file="nvt.gro" ftype="gro" compare="sim_size"/>
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157 <output name="output2" file="nvt.cpt" ftype="cpt" compare="sim_size"/>
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158 </test>
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159 </tests>
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160 <help><![CDATA[
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161
1
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162 Upload GRO, TOP and ITP (position restraint) files for equilibration under an NVT ensemble. To take advantage of all GROMACS features, upload an MDP file with simulation parameters. Otherwise, choose parameters through the Galaxy interface. See http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html for more information on the options.
0
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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163 ]]></help>
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164
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165 <expand macro="citations" />
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166 </tool>