Mercurial > repos > chemteam > gmx_solvate

comparison solvate.xml @ 3:7161b230adad draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:47:31 -0400
parents 77aaf9a68166
children cdacad684da1
comparison
equal deleted inserted replaced
2:b37a1d7bf6c2 3:7161b230adad
35 rvdw = 1.0 35 rvdw = 1.0
36 pbc = xyz 36 pbc = xyz
37 </configfile> 37 </configfile>
38 </configfiles> 38 </configfiles>
39 <inputs> 39 <inputs>
40 <param argument="gro_input" type="data" format='gro' label="GRO structure file."/> 40 <param argument="gro_input" type="data" format='gro' label="GRO structure file"/>
41 <param argument="top_input" type="data" format='top' label="Topology (TOP) file."/> 41 <param argument="top_input" type="data" format='top' label="Topology (TOP) file"/>
42 <param name="water_model" type="select" label="Water model for solvation."> 42 <param name="water_model" type="select" label="Water model for solvation">
43 <option value="tip3p">TIP3P</option> 43 <option value="tip3p">TIP3P</option>
44 <option value="tip4p">TIP4P</option> 44 <option value="tip4p">TIP4P</option>
45 <option value="spc216">SPC</option> 45 <option value="spc216">SPC</option>
46 </param> 46 </param>
47 <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/> 47 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/>
48 48
49 </inputs> 49 </inputs>
50 <outputs> 50 <outputs>
51 <data name="output1" format="gro" from_work_dir="solv_ions.gro"/> 51 <data name="output1" format="gro" from_work_dir="solv_ions.gro"/>
52 <data name="output2" format="top" from_work_dir="./top_input.top"/> 52 <data name="output2" format="top" from_work_dir="./top_input.top"/>
63 <output name="output2" file="topol_solv.top" ftype="top"/> 63 <output name="output2" file="topol_solv.top" ftype="top"/>
64 </test> 64 </test>
65 </tests> 65 </tests>
66 <help><![CDATA[ 66 <help><![CDATA[
67 67
68 Select a water model - consistent with the one selected in system set-up and provide GRO and TOP files to be updated with the added water molecules. In addition, sodium or chloride ions are added if necessary to ensure the system is charge-neutral. 68 .. class:: infomark
69
70 **What it does**
71
72 This tool solvates a system prior to a GROMACS simulation. In addition, sodium or chloride ions will be added if necessary to ensure the system is charge-neutral.
73
74 _____
75
76 .. class:: infomark
77
78 **Input**
79
80 - GRO structure file.
81 - Topology (TOP) file.
82
83 In addition, a water model must be selected - this should be consistent with the one selected previously in the system setup.
84
85 _____
86
87
88 .. class:: infomark
89
90 **Output**
91
92 - GRO structure file.
69 93
70 ]]></help> 94 ]]></help>
71 95
72 <expand macro="citations" /> 96 <expand macro="citations" />
73 </tool> 97 </tool>