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annotate minim.xml @ 1:ce6a81f37756 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
author chemteam
date Thu, 04 Oct 2018 18:17:26 -0400
parents 3158b8b4e981
children 0725fe83f0df
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3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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1 <tool id="gmx_em" name="GROMACS energy minimization" version="@VERSION@">
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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2 <description>of the system prior to equilibration and production MD</description>
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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3 <macros>
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4 <import>macros.xml</import>
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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5 </macros>
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3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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7 <expand macro="requirements" />
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9 <command detect_errors="exit_code"><![CDATA[
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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11 #if $mdp.mdpfile == 'custom':
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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12 ln -s '$mdp.mdp_input' ./minim.mdp &&
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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13 #else:
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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14 ln -s '$minim' ./minim.mdp &&
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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15 #end if
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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17 ln -s '$gro_input' ./solv_ions.gro &&
3158b8b4e981 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 &&
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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20 gmx grompp -f ./minim.mdp -c ./solv_ions.gro -p ./top_input.top -o em.tpr &>> verbose.txt &&
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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21 gmx mdrun -deffnm em &>> verbose.txt
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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22
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23 ]]></command>
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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24 <configfiles>
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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25 <!-- .mdp files for the gromacs simulation -->
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26 <configfile name="minim">
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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27 #if $mdp.mdpfile == 'default':
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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28 ; minim.mdp - used as input into grompp to generate em.tpr
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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29 integrator = $mdp.integrator ; Algorithm (steep = steepest descent minimization)
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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30 emtol = $mdp.emtol ; Stop minimization when the maximum force is less than this value
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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31 emstep = $mdp.emstep ; Energy step size
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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32 nsteps = $mdp.md_steps ; Maximum number of (minimization) steps to perform
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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33
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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34 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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35 nstlist = 1 ; Frequency to update the neighbor list and long range forces
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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36 cutoff-scheme = $mdp.cutoffscheme
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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37 ns_type = grid ; Method to determine neighbor list (simple, grid)
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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38 coulombtype = $mdp.coulombtype ; Treatment of long range electrostatic interactions
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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39 rcoulomb = $mdp.rcoulomb ; Short-range electrostatic cut-off
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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40 rlist = $mdp.rlist ; Cut-off distance for the short-range neighbor list.
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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41 rvdw = $mdp.rvdw ; Short-range Van der Waals cut-off
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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42 pbc = xyz ; Periodic Boundary Conditions (yes/no)
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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43 #end if
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44 </configfile>
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45 </configfiles>
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46
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47 <inputs>
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48 <param argument="gro_input" type="data" format='gro' label="GRO structure file."/>
3158b8b4e981 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."/>
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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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."/>
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51
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52 <conditional name="mdp">
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53 <param name="mdpfile" type="select" label="Parameter input">
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54 <option value="custom">Upload own MDP file</option>
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55 <option value="default">Use default (partially customisable) setting</option>
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56 </param>
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57 <when value="custom">
3158b8b4e981 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)."/>
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59 </when>
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60
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61 <when value="default">
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62 <param argument="integrator" type="select" label="Choice of integrator.">
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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63 <option value="steep">Steepest descent algorithm.</option>
3158b8b4e981 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>
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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65 <option value="l-bfgs">Quasi-Newtonian algorithm.</option>
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66 </param>
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67 <param argument="cutoffscheme" type="select" label="Neighbor searching.">
3158b8b4e981 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>
3158b8b4e981 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>
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70 </param>
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71 <param argument="coulombtype" type="select" label="Electrostatics.">
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72 <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option>
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73 <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option>
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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74 <option value="Reaction-Field-zero">Reaction field electrostatics.</option>
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75 </param>
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76 <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/>
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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."/>
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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78 <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/>
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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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" />
3158b8b4e981 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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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>