Mercurial > repos > chemteam > gmx_solvate

annotate solvate.xml @ 13:ae87e7b2454c draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit ab7232ec03a3361f808f5a0be0828e0f7fbd376d"
author chemteam
date Mon, 23 Nov 2020 10:47:29 +0000
parents e205c82e9959
children 2c8ed1b52bf7
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27ea4e1a3f95 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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1 <tool id="gmx_solvate" name="GROMACS solvation and adding ions" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>to structure and topology files</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="@GALAXY_VERSION@">0</token>
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6 </macros>
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8 <expand macro="requirements" />
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10 <command detect_errors="exit_code"><![CDATA[
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12 ln -s '$ions' ./ions.mdp &&
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13 ln -s '$gro_input' ./gro_input.gro &&
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14 ln -s '$top_input' ./top_input.top &&
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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e205c82e9959 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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16 gmx solvate -cp ./gro_input.gro -cs ${water_model}.gro -o solv.gro -p ./top_input.top &>> verbose.txt &&
e205c82e9959 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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17 gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr &>> verbose.txt
e205c82e9959 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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18 #if $neutralise and $conc: ## else this step would do nothing
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19 &&
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20 echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL $neutralise -conc $conc &>> verbose.txt &&
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21 mv solv_ions.gro solv.gro
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22 #end if
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24 ]]></command>
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25 <configfiles>
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26 <!-- .mdp file for the gromacs simulation -->
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27 <configfile name="ions">
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27ea4e1a3f95 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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29 ; Parameters are not so important here as no simulation is run
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30 integrator = steep
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31 emtol = 1000.0
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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32 emstep = 0.01
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33 nsteps = 1
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34 nstlist = 1
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35 cutoff-scheme = Verlet
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36 ns_type = grid
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37 coulombtype = cutoff
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38 rcoulomb = 1.0
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39 rvdw = 1.0
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40 pbc = xyz
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41 </configfile>
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42 </configfiles>
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43 <inputs>
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44 <param argument="gro_input" type="data" format='gro' label="GRO structure file"/>
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45 <param argument="top_input" type="data" format='top' label="Topology (TOP) file"/>
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46 <param name="water_model" type="select" label="Water model for solvation" help="Note SPC is a generic equilibrated 3-point solvent model and can be used as the solvent configuration for any of SPC, SPC/E, or TIP3P water.">
cdacad684da1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 10f45d117e34624bceb32442742ae0b8eb2dae30"
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47 <option value="spc216" selected="true">SPC (generic three-point model)</option>
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48 <option value="tip4p">TIP4P (four-point model)</option>
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49 <option value="tip5p">TIP5P (five-point model)</option>
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50 </param>
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51 <param name="neutralise" label="Add ions to neutralise system?" type="select" help="If system is charged, replace an appropriate number of randomly selected solvent molecules with sodium or chloride ions to neutralise it.">
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52 <option value="-neutral">Yes, add ions</option>
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53 <option value="">No</option>
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54 </param>
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55
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56 <param argument="conc" type="float" value="0" min="0" max="6" label="Specify salt concentration (sodium chloride) to add, in mol/liter" help="Note existing ions in the system are not taken into account - including those added if the neutralise option is selected. Ions are added by randomly replacing water molecules." />
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57
5
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58 <expand macro="log" />
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59
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60 </inputs>
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61 <outputs>
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62 <data name="output1" format="gro" from_work_dir="solv.gro"/>
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63 <data name="output2" format="top" from_work_dir="./top_input.top"/>
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64 <expand macro="log_outputs" />
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65 </outputs>
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66 <tests>
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67 <test>
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68 <param name="gro_input" value="newbox.gro" />
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69 <param name="neutralise" value="-neutral" />
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70 <param name="top_input" value="topol.top" />
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71 <param name="water_model" value="spc216" />
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72 <param name="conc" value="1" />
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73 <output name="output1" ftype="gro">
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74 <!-- replacement of water with ions is random, thus we cannot compare the whole file -->
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75 <assert_contents>
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76 <has_text text="1.671 1.591 3.533"/>
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77 <has_text text="2.032 2.417 1.345"/>
27ea4e1a3f95 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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78 <has_text text="3.438 1.662 0.307"/>
27ea4e1a3f95 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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79 <has_text text="2218CL"/>
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80 <has_text text="2147NA"/>
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81 </assert_contents>
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82 </output>
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83 <output name="output2" file="topol_solv.top" ftype="top" lines_diff="4">
27ea4e1a3f95 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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84 <assert_contents>
27ea4e1a3f95 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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85 <has_line line="SOL 2130" />
27ea4e1a3f95 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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86 <has_line line="NA 41" />
27ea4e1a3f95 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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87 <has_line line="CL 43" />
27ea4e1a3f95 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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88 </assert_contents>
27ea4e1a3f95 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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89 </output>
0
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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90 </test>
5
645139abefae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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91 <test>
645139abefae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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92 <param name="gro_input" value="newbox.gro" />
12
e205c82e9959 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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93 <param name="neutralise" value="" />
11
27ea4e1a3f95 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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94 <param name="top_input" value="topol.top"/>
5
645139abefae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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95 <param name="water_model" value="spc216" />
11
27ea4e1a3f95 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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96 <param name="conc" value="0" />
27ea4e1a3f95 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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97 <output name="output1" ftype="gro">
27ea4e1a3f95 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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98 <assert_contents>
27ea4e1a3f95 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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99 <has_text text="1.671 1.591 3.533"/>
27ea4e1a3f95 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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100 <has_text text="2.032 2.417 1.345"/>
27ea4e1a3f95 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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101 <has_text text="3.438 1.662 0.307"/>
27ea4e1a3f95 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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102 <not_has_text text="2218CL"/>
27ea4e1a3f95 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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103 </assert_contents>
27ea4e1a3f95 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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104 </output>
5
645139abefae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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105 </test>
0
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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106 </tests>
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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107 <help><![CDATA[
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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108
3
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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109 .. class:: infomark
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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110
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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111 **What it does**
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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112
11
27ea4e1a3f95 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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113 This tool solvates a system prior to a GROMACS simulation. In addition, sodium or chloride ions can be added if necessary to ensure the system is charge-neutral.
3
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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114
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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115 _____
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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116
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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117 .. class:: infomark
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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118
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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119 **Input**
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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120
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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121 - GRO structure file.
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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122 - Topology (TOP) file.
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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123
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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124 In addition, a water model must be selected - this should be consistent with the one selected previously in the system setup.
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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125
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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126 _____
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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127
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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128
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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129 .. class:: infomark
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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130
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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131 **Output**
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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132
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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133 - GRO structure file.
0
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134
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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135 ]]></help>
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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136
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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137 <expand macro="citations" />
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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138 </tool>