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annotate nvt.xml @ 3:f8a5a4b7cd86 draft default tip

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit b1b74e91a242f2de250761a79b17d77e68b1045f"
author chemteam
date Fri, 30 Aug 2019 14:59:59 -0400
parents 2636ff4c9964
children
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5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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1 <tool id="gmx_nvt" name="GROMACS NVT equilibration" version="@VERSION@">
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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2 <description>- constant-temperature and -volume equilibration of a system</description>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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3 <macros>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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4 <import>macros.xml</import>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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5 </macros>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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6
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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7 <expand macro="requirements" />
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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8
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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9 <command detect_errors="exit_code"><![CDATA[
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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10 #if $mdp.mdpfile == "custom":
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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11 ln -s '$mdp.mdp_input' ./nvt.mdp &&
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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12 #end if
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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13 #if $mdp.mdpfile == "default":
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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14 ln -s '$nvt' ./nvt.mdp &&
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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15 #end if
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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16
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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17 ln -s '$gro_input' ./em.gro &&
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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18 ln -s '$top_input' ./top_input.top &&
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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19 ln -s '$itp_input' ./posres.itp &&
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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20
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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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 &&
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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22 gmx mdrun -deffnm nvt &>> verbose.txt
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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23
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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24 #if $str == 'pdb' or $str == 'both'
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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25 && gmx editconf -f nvt.gro -o nvt.pdb &>> verbose.txt
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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26 #end if
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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27 ]]></command>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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28 <configfiles>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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29 <!-- .mdp file for the gromacs simulation -->
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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30 <configfile name="nvt">
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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31 #if $mdp.mdpfile == 'default':
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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32 title = NVT equilibration
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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33 define = -DPOSRES ; position restrain the protein
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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34 ; Run parameters
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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35 integrator = $mdp.integrator ; leap-frog integrator
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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36 nsteps = $mdp.md_steps ; 2 * 50000 = 100 ps
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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37 dt = $mdp.step_length ; 2 fs
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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38 ; Output control
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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39 nstxout = $mdp.write_freq ; save coordinates every n ps
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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40 nstvout = $mdp.write_freq ; save velocities every n ps
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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41 nstenergy = $mdp.write_freq ; save energies every n ps
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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42 nstlog = $mdp.write_freq ; update log file every n ps
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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43 nstxout-compressed = $mdp.write_freq ; save compressed coordinates every 10.0 ps
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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44 ; Bond parameters
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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45 continuation = no ; first dynamics run
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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46 constraint_algorithm = lincs ; holonomic constraints
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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47 constraints = $mdp.constraints ; all bonds (even heavy atom-H bonds) constrained
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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48 lincs_iter = 1 ; accuracy of LINCS
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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49 lincs_order = 4 ; also related to accuracy
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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50 ; Neighborsearching
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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51 cutoff-scheme = $mdp.cutoffscheme
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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52 ns_type = grid ; search neighboring grid cells
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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53 nstlist = 10 ; 20 fs, largely irrelevant with Verlet
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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54 rcoulomb = $mdp.rcoulomb ; Short-range electrostatic cut-off
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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55 rlist = $mdp.rlist ; Cut-off distance for the short-range neighbor list.
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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56 rvdw = $mdp.rvdw ; Short-range Van der Waals cut-off
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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57 ; Electrostatics
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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58 coulombtype = $mdp.coulombtype ; method for electrostatics calculations e.g. PME
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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59 pme_order = 4 ; cubic interpolation
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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60 fourierspacing = 0.16 ; grid spacing for FFT
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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61 ; Temperature coupling is on
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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62 tcoupl = V-rescale ; modified Berendsen thermostat
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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63 tc-grps = Protein Non-Protein ; two coupling groups - more accurate
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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64 tau_t = 0.1 0.1 ; time constant, in ps
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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65 ref_t = $mdp.temperature $mdp.temperature ; reference temperature, one for each group, in K
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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66 ; Pressure coupling is off
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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67 pcoupl = no ; no pressure coupling in NVT
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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68 ; Periodic boundary conditions
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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69 pbc = xyz ; 3-D PBC
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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70 ; Dispersion correction
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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71 DispCorr = EnerPres ; account for cut-off vdW scheme
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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72 ; Velocity generation
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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73 gen_vel = yes ; assign velocities from Maxwell distribution
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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74 gen_temp = 300 ; temperature for Maxwell distribution
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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75 gen_seed = -1 ; generate a random seed
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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76 #end if
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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77 </configfile>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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78
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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79 </configfiles>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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80 <inputs>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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81 <param argument="gro_input" type="data" format='gro' label="GRO structure file."/>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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82 <param argument="top_input" type="data" format='top' label="Topology (TOP) file."/>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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83 <param argument="itp_input" type="data" format='itp' label="Position restraint file."/>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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84
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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85 <expand macro="md_inputs"/>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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86 </inputs>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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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>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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90 </data>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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91 <data name="output5" format="pdb" from_work_dir="nvt.pdb">
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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92 <filter>str == 'pdb' or str == 'both'</filter>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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93 </data>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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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">
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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96 <filter>traj == 'trr' or traj == 'both'</filter>
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97 </data>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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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>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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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>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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104 </outputs>
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105 <tests>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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106 <test>
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107 <param name="gro_input" value="em.gro" />
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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108 <param name="top_input" value="topol_solv.top" />
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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109 <param name="itp_input" value="posres.itp" />
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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110 <param name="traj" value="xtc"/>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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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"/>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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116 <output name="output2" file="nvt.cpt" ftype="cpt" compare="sim_size"/>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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117 <output name="output4" file="nvt.xtc" ftype="xtc" compare="sim_size"/>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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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" />
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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123 <param name="top_input" value="topol_solv.top" />
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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124 <param name="itp_input" value="posres.itp" />
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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125 <param name="traj" value="xtc"/>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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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"/>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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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" />
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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137 <param name="top_input" value="topol_solv.top" />
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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138 <param name="itp_input" value="posres.itp" />
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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139 <param name="str" value="gro"/>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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140 <param name="traj" value="trr"/>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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141
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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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"/>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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146 <output name="output3" file="nvt.trr" ftype="trr" compare="sim_size"/>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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147 </test>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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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" />
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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152 <param name="mdpfile" value="custom" />
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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153 <param name="mdp_input" value="nvt.mdp" />
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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154 <param name="traj" value="none"/>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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155 <param name="str" value="gro"/>
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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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
2
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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
5e6de964529f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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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>