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newmods.xml
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newmods.xml
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<tool id="gmx_solvate" name="GROMACS new mods to IM" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
<description>to structure and topology files</description>
<macros>
<import>macros.xml</import>
<token name="@GALAXY_VERSION@">0</token>
</macros>
<expand macro="requirements" />
<command detect_errors="exit_code"><![CDATA[
ln -s '$ions' ./ions.mdp &&
ln -s '$gro_input' ./gro_input.gro &&
ln -s '$top_input' ./top_input.top &&
ln -s '$mol_input' ./mol_input.gro &&
gmx insert-molecules -f ./gro_input.gro -ci ./mol_input.gro -o multiples.gro -nmol '$nmols'
#if $box.config == "true":
-box $box.dim
#end if
&>> verbose.txt
]]></command>
<configfiles>
<!-- .mdp file for the gromacs simulation -->
<configfile name="ions">
; Parameters are not so important here as no simulation is run
integrator = steep
emtol = 1000.0
emstep = 0.01
nsteps = 1
nstlist = 1
cutoff-scheme = Verlet
ns_type = grid
coulombtype = cutoff
rcoulomb = 1.0
rvdw = 1.0
pbc = xyz
</configfile>
</configfiles>
<inputs>
<param argument="gro_input" type="data" format='gro' label="GRO structure file"/>
<param argument="top_input" type="data" format='top' label="Topology (TOP) file"/>
<param argument="mol_input" type="data" format='gro' label="Inserting molecule's GRO structure file"/>
<param name="nmols" type="integer" value="0" min="0" label="Number of copies of the molecule to add to system"/>
<conditional name="box">
<param argument="config" type="select" label="Change box size?">
<option value="true">Yes</option>
<option value="false" selected="true">No</option>
</param>
<when value="true">
<param argument="dim" type="float" label="New box dimensions in nanometers" value="0.0" min="0.0" max="10.0" help="Dimensions of the new box size. This is useful if you're adding a lot of molecules that may not fit inside the original box size. These dimensions, and box type can always be changed later with gmx_editconf" />
</when>
<when value="false"/>
</conditional>
</inputs>
<outputs>
<data name="output1" format="gro" from_work_dir="multiples.gro" label="GROMACS inserted-molecules (GRO) on ${on_string}"/>
<data name="output2" format="top" from_work_dir="./top_input.top" label="GROMACS inserted-molecules (TOP) on ${on_string}"/>
<expand macro="log_outputs" />
</outputs>
<tests>
<test>
<param name="gro_input" value="newbox.gro" />
<param name="neutralise" value="-neutral" />
<param name="top_input" value="topol.top" />
<param name="water_model" value="spc216" />
<param name="conc" value="1" />
<output name="output1" ftype="gro">
<!-- file is big, thus we do not compare the whole file -->
<assert_contents>
<has_text text="1.671 1.591 3.533"/>
<has_text text="2.032 2.417 1.345"/>
<has_text text="3.438 1.662 0.307"/>
<has_text text="2218CL"/>
<has_text text="2147NA"/>
</assert_contents>
</output>
<output name="output2" ftype="top">
<assert_contents>
<has_line line="SOL 2130" />
<has_line line="NA 41" />
<has_line line="CL 43" />
</assert_contents>
</output>
</test>
<test>
<param name="gro_input" value="newbox.gro" />
<param name="neutralise" value="" />
<param name="top_input" value="topol.top"/>
<param name="water_model" value="spc216" />
<param name="conc" value="0" />
<output name="output1" ftype="gro">
<assert_contents>
<has_text text="1.671 1.591 3.533"/>
<has_text text="2.032 2.417 1.345"/>
<has_text text="3.438 1.662 0.307"/>
<not_has_text text="2218CL"/>
</assert_contents>
</output>
</test>
</tests>
<help><![CDATA[
.. class:: infomark
**What it does**
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.
_____
.. class:: infomark
**Input**
- GRO structure file.
- Topology (TOP) file.
In addition, a water model must be selected - this should be consistent with the one selected previously in the system setup.
_____
.. class:: infomark
**Output**
- GRO structure file.
]]></help>
<expand macro="citations" />
</tool>