Mercurial > repos > chemteam > gmx_solvate
comparison solvate.xml @ 3:7161b230adad draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author | chemteam |
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date | Mon, 07 Oct 2019 12:47:31 -0400 |
parents | 77aaf9a68166 |
children | cdacad684da1 |
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2:b37a1d7bf6c2 | 3:7161b230adad |
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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> |