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annotate npt.xml @ 3:b8957099f695 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 14:59:12 -0400
parents ca54cbe47f45
children
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97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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1 <tool id="gmx_npt" name="GROMACS NPT equilibration" version="@VERSION@">
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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2 <description>- constant-temperature and -pressure equilibration of a system</description>
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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3 <macros>
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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4 <import>macros.xml</import>
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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5 </macros>
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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6
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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7 <expand macro="requirements" />
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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8
97fe2fa79964 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[
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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10 #if $mdp.mdpfile == "custom":
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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11 ln -s '$mdp.mdp_input' ./npt.mdp &&
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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12 #end if
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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13 #if $mdp.mdpfile == "default":
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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14 ln -s '$npt' ./npt.mdp &&
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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15 #end if
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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16
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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17 ln -s '$gro_input' ./nvt.gro &&
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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18 ln -s '$cpt_input' ./nvt.cpt &&
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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19 ln -s '$top_input' ./top_input.top &&
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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20 ln -s '$itp_input' ./posres.itp &&
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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21
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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22 gmx grompp -f ./npt.mdp -c ./nvt.gro -r ./nvt.gro -t ./nvt.cpt -p ./top_input.top -o npt.tpr &>> verbose.txt &&
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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23 gmx mdrun -deffnm npt &>> verbose.txt
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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24
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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25 #if $str == 'pdb' or $str == 'both'
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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26 && gmx editconf -f npt.gro -o npt.pdb &>> verbose.txt
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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27 #end if
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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28
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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29 ]]></command>
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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30 <configfiles>
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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31 <!-- .mdp file for the gromacs simulation -->
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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32 <configfile name="npt">
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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33 #if $mdp.mdpfile == 'default':
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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34 title = NPT equilibration
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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35 define = -DPOSRES ; position restrain the protein
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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36 ; Run parameters
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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37 integrator = $mdp.integrator ; leap-frog integrator
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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38 nsteps = $mdp.md_steps ; 2 * 50000 = 100 ps
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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39 dt = $mdp.step_length ; 2 fs
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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40 ; Output control
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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41 nstxout = $mdp.write_freq ; save coordinates every 1.0 ps
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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42 nstvout = $mdp.write_freq ; save velocities every 1.0 ps
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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43 nstenergy = $mdp.write_freq ; save energies every 1.0 ps
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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44 nstlog = $mdp.write_freq ; update log file every 1.0 ps
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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45 nstxout-compressed = $mdp.write_freq ; save compressed coordinates every 10.0 ps
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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46
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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47 ; Bond parameters
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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48 continuation = yes ; Restarting after NVT
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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49 constraint_algorithm = lincs ; holonomic constraints
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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50 constraints = $mdp.constraints ; all bonds (even heavy atom-H bonds) constrained
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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51 lincs_iter = 1 ; accuracy of LINCS
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52 lincs_order = 4 ; also related to accuracy
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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53 ; Neighborsearching
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54 cutoff-scheme = $mdp.cutoffscheme
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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55 ns_type = grid ; search neighboring grid cells
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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56 nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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57 rcoulomb = $mdp.rcoulomb ; Short-range electrostatic cut-off
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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58 rlist = $mdp.rlist ; Cut-off distance for the short-range neighbor list.
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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59 rvdw = $mdp.rvdw ; Short-range Van der Waals cut-off
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60 ; Electrostatics
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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61 coulombtype = $mdp.coulombtype ; method for electrostatics calculations e.g. PME
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62 pme_order = 4 ; cubic interpolation
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63 fourierspacing = 0.16 ; grid spacing for FFT
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64 ; Temperature coupling is on
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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65 tcoupl = V-rescale ; modified Berendsen thermostat
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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66 tc-grps = Protein Non-Protein ; two coupling groups - more accurate
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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67 tau_t = 0.1 0.1 ; time constant, in ps
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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68 ref_t = $mdp.temperature $mdp.temperature ; reference temperature, one for each group, in K
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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69 ; Pressure coupling is on
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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70 pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
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71 pcoupltype = isotropic ; uniform scaling of box vectors
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72 tau_p = 2.0 ; time constant, in ps
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73 ref_p = 1.0 ; reference pressure, in bar
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74 compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
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75 refcoord_scaling = com
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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76 ; Periodic boundary conditions
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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77 pbc = xyz ; 3-D PBC
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78 ; Dispersion correction
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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79 DispCorr = EnerPres ; account for cut-off vdW scheme
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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80 ; Velocity generation
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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81 gen_vel = no ; Velocity generation is off
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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82 #end if
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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83 </configfile>
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84
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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85 </configfiles>
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86 <inputs>
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87 <param argument="gro_input" type="data" format='gro' label="GRO structure file."/>
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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88 <param argument="top_input" type="data" format='top' label="Topology (TOP) file."/>
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89 <param argument="cpt_input" type="data" format='cpt' label="Checkpoint (CPT) file from NVT run."/>
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90 <param argument="itp_input" type="data" format='itp' label="Position restraint file."/>
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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91
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92 <expand macro="md_inputs"/>
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93 </inputs>
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94 <outputs>
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95 <data name="output1" format="gro" from_work_dir="npt.gro">
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96 <filter>str == 'gro' or str == 'both'</filter>
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97 </data>
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98 <data name="output5" format="pdb" from_work_dir="npt.pdb">
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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99 <filter>str == 'pdb' or str == 'both'</filter>
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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100 </data>
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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101 <data name="output2" format="cpt" from_work_dir="npt.cpt"/>
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102 <data name="output3" format="trr" from_work_dir="npt.trr">
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103 <filter>traj == 'trr' or traj == 'both'</filter>
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104 </data>
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105 <data name="output4" format="xtc" from_work_dir="npt.xtc">
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106 <filter>traj == 'xtc' or traj == 'both'</filter>
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107 </data>
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108 <data name="report" format="txt" from_work_dir="verbose.txt">
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109 <filter>capture_log</filter>
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110 </data>
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111 </outputs>
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112
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113 <tests>
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114 <test>
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115 <param name="gro_input" value="nvt.gro" />
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116 <param name="top_input" value="topol_solv.top" />
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117 <param name="cpt_input" value="nvt.cpt" />
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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118 <param name="itp_input" value="posres.itp" />
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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119 <param name="traj" value="xtc"/>
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120 <param name="str" value="both"/>
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121
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122 <expand macro="test_params"/>
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123
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124 <output name="output1" file="npt.gro" ftype="gro" compare="sim_size"/>
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125 <output name="output2" file="npt.cpt" ftype="cpt" compare="sim_size"/>
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126 <output name="output4" file="npt.xtc" ftype="xtc" compare="sim_size"/>
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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127 <output name="output5" file="npt.pdb" ftype="pdb" compare="sim_size"/>
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128 </test>
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129
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130 <test>
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131 <param name="gro_input" value="nvt.gro" />
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132 <param name="top_input" value="topol_solv.top" />
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133 <param name="cpt_input" value="nvt.cpt" />
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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134 <param name="itp_input" value="posres.itp" />
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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135 <param name="traj" value="xtc"/>
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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136 <param name="str" value="pdb"/>
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137
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138 <expand macro="test_params"/>
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139
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140 <output name="output2" file="npt.cpt" ftype="cpt" compare="sim_size"/>
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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141 <output name="output4" file="npt.xtc" ftype="xtc" compare="sim_size"/>
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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142 <output name="output5" file="npt.pdb" ftype="pdb" compare="sim_size"/>
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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143 </test>
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144
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145 <test>
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146 <param name="gro_input" value="nvt.gro" />
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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147 <param name="top_input" value="topol_solv.top" />
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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148 <param name="cpt_input" value="nvt.cpt" />
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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149 <param name="itp_input" value="posres.itp" />
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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150 <param name="str" value="none"/>
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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151 <param name="traj" value="trr"/>
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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152
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153 <expand macro="test_params"/>
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154
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155 <output name="output2" file="npt.cpt" ftype="cpt" compare="sim_size"/>
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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156 <output name="output3" file="npt.trr" ftype="trr" compare="sim_size"/>
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157 </test>
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158
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159 <test>
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160 <param name="gro_input" value="nvt.gro" />
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161 <param name="top_input" value="topol_solv.top" />
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162 <param name="cpt_input" value="nvt.cpt" />
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163 <param name="itp_input" value="posres.itp" />
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164 <param name="mdpfile" value="custom" />
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165 <param name="mdp_input" value="npt.mdp" />
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166 <param name="traj" value="none"/>
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167 <param name="str" value="gro"/>
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168 <output name="output1" file="npt.gro" ftype="gro" compare="sim_size"/>
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169 <output name="output2" file="npt.cpt" ftype="cpt" compare="sim_size"/>
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170 </test>
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171 </tests>
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172 <help><![CDATA[
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173
2
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174 Upload GRO, TOP and ITP (position restraint) files for equilibration under an NPT ensemble, as well as the checkpoint (CPT) file from the NVT equilibration. To take advantage of all GROMACS features, upload an MDP file with simulation parameters. Otherwise, choose parameters through the Galaxy interface. See http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html for more information on the options.
0
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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175
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176 ]]></help>
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97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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178 <expand macro="citations" />
97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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97fe2fa79964 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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180 </tool>