Mercurial > repos > chemteam > gmx_em
annotate minim.xml @ 0:911eb71ccd1f draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
author | chemteam |
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date | Thu, 04 Oct 2018 17:39:57 -0400 |
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children | ea7b9183bf30 |
rev | line source |
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911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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changeset
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1 <tool id="gmx_em" name="GROMACS energy minimization" version="@VERSION@"> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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2 <description>of the system prior to equilibration and production MD</description> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
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3 <macros> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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4 <import>macros.xml</import> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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5 </macros> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
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6 |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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7 <expand macro="requirements" /> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
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8 |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
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9 <command detect_errors="exit_code"><![CDATA[ |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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10 |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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11 #if $mdp.mdpfile == 'custom': |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
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12 ln -s '$mdp.mdp_input' ./minim.mdp && |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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13 #else: |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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14 ln -s '$minim' ./minim.mdp && |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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15 #end if |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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16 |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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17 ln -s '$gro_input' ./solv_ions.gro && |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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18 ln -s '$top_input' ./top_input.top && |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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19 |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
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20 gmx grompp -f ./minim.mdp -c ./solv_ions.gro -p ./top_input.top -o em.tpr &>> verbose.txt && |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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21 gmx mdrun -deffnm em &>> verbose.txt |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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22 |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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23 ]]></command> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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changeset
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24 <configfiles> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff
changeset
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25 <!-- .mdp files for the gromacs simulation --> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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changeset
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26 <configfile name="minim"> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff
changeset
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27 #if $mdp.mdpfile == 'default': |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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28 ; minim.mdp - used as input into grompp to generate em.tpr |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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29 integrator = $mdp.integrator ; Algorithm (steep = steepest descent minimization) |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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30 emtol = $mdp.emtol ; Stop minimization when the maximum force is less than this value |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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31 emstep = $mdp.emstep ; Energy step size |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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32 nsteps = $mdp.md_steps ; Maximum number of (minimization) steps to perform |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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33 |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
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34 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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35 nstlist = 1 ; Frequency to update the neighbor list and long range forces |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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36 cutoff-scheme = $mdp.cutoffscheme |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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37 ns_type = grid ; Method to determine neighbor list (simple, grid) |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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38 coulombtype = $mdp.coulombtype ; Treatment of long range electrostatic interactions |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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39 rcoulomb = $mdp.rcoulomb ; Short-range electrostatic cut-off |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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40 rlist = $mdp.rlist ; Cut-off distance for the short-range neighbor list. |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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41 rvdw = $mdp.rvdw ; Short-range Van der Waals cut-off |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
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42 pbc = xyz ; Periodic Boundary Conditions (yes/no) |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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43 #end if |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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parents:
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44 </configfile> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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45 </configfiles> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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46 |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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47 <inputs> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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48 <param argument="gro_input" type="data" format='gro' label="GRO structure file."/> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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49 <param argument="top_input" type="data" format='top' label="Topology (TOP) file."/> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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parents:
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50 <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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51 |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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52 <conditional name="mdp"> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
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53 <param name="mdpfile" type="select" label="Parameter input"> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
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54 <option value="custom">Upload own MDP file</option> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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55 <option value="default">Use default (partially customisable) setting</option> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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56 </param> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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57 <when value="custom"> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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58 <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)."/> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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parents:
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59 </when> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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60 |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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61 <when value="default"> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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62 <param argument="integrator" type="select" label="Choice of integrator."> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
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63 <option value="steep">Steepest descent algorithm.</option> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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64 <option value="cg">Conjugate gradient algorithm.</option> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
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65 <option value="l-bfgs">Quasi-Newtonian algorithm.</option> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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66 </param> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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67 <param argument="cutoffscheme" type="select" label="Neighbor searching."> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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68 <option value="Verlet">Generate a pair list with buffering.</option> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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69 <option value="group">Generate a pair list for groups of atoms.</option> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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70 </param> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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71 <param argument="coulombtype" type="select" label="Electrostatics."> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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72 <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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73 <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
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74 <option value="Reaction-Field-zero">Reaction field electrostatics.</option> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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75 </param> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
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76 <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
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77 <param argument="rlist" value="1.0" type="float" label="Cut-off distance for the short-range neighbor list. Ignored if the Verlet cutoff scheme is set."/> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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78 <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
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79 <param argument="md_steps" type="integer" label="Number of steps for the MD simulation" value="0" min="0" max="1000000" help="MD steps" /> |
911eb71ccd1f
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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80 <param argument="emtol" type="float" label="EM tolerance" value="0" min="0" max="10000" help="The minimization is converged when the maximum force is smaller than this value" /> |
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81 <param argument="emstep" type="float" label="Maximum step size /nm" value="0.01" min="0.0001" max="1.0" help="Initial step size in nm." /> |
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82 </when> |
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83 </conditional> |
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84 </inputs> |
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85 <outputs> |
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86 <data name="output1" format="gro" from_work_dir="em.gro"/> |
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87 <data name="report" format="txt" from_work_dir="verbose.txt"> |
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88 <filter>capture_log</filter> |
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89 </data> |
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90 </outputs> |
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91 <tests> |
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92 <test> |
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93 <param name="gro_input" value="solv_ions.gro" /> |
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94 <param name="top_input" value="topol_solv.top" /> |
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95 <param name="mdpfile" value="default" /> |
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96 <param name="integrator" value="steep" /> |
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97 <param name="cutoffscheme" value="Verlet" /> |
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98 <param name="coulombtype" value="PME" /> |
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99 <param name="rcoulomb" value="1.0" /> |
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100 <param name="rlist" value="1.0" /> |
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101 <param name="md_steps" value="50000" /> |
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102 <param name="emtol" value="1000.0" /> |
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103 <param name="emstep" value="0.01" /> |
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104 |
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105 <output name="output1" file="em.gro" ftype="gro" compare="sim_size"/> |
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106 </test> |
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107 <test> |
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108 <param name="gro_input" value="solv_ions.gro" /> |
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109 <param name="top_input" value="topol_solv.top" /> |
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110 <param name="mdpfile" value="custom" /> |
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111 <param name="mdp_input" value="minim.mdp" /> |
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112 <output name="output1" file="em.gro" ftype="gro" compare="sim_size"/> |
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113 </test> |
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114 |
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115 </tests> |
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116 <help><![CDATA[ |
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117 |
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118 Upload GRO and TOP files for energy minimisation. 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/online/mdp_opt.html for more information on the options. |
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119 |
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120 ]]></help> |
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121 |
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122 <expand macro="citations" /> |
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123 </tool> |