diff solvate.xml @ 4:cdacad684da1 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 10f45d117e34624bceb32442742ae0b8eb2dae30"
author chemteam
date Wed, 30 Oct 2019 13:32:37 -0400
parents 7161b230adad
children 645139abefae
line wrap: on
line diff
--- a/solvate.xml	Mon Oct 07 12:47:31 2019 -0400
+++ b/solvate.xml	Wed Oct 30 13:32:37 2019 -0400
@@ -14,7 +14,7 @@
 
         gmx solvate -cp ./gro_input.gro -cs ${water_model}.gro -o solv.gro -p ./top_input.top &>> verbose.txt &&
 
-        gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr -maxwarn 1 &>> verbose.txt &&
+        gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr &>> verbose.txt &&
 
         echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL -neutral &>> verbose.txt
     
@@ -30,7 +30,7 @@
 nstlist        = 1
 cutoff-scheme   = Verlet
 ns_type        = grid
-coulombtype      = PME
+coulombtype      = cutoff
 rcoulomb      = 1.0
 rvdw        = 1.0
 pbc            = xyz
@@ -39,10 +39,10 @@
     <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 name="water_model" type="select"  label="Water model for solvation">
-            <option value="tip3p">TIP3P</option>
-            <option value="tip4p">TIP4P</option>
-            <option value="spc216">SPC</option>
+        <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.">
+            <option value="spc216" selected="true">SPC (generic three-point model)</option>
+            <option value="tip4p">TIP4P (four-point model)</option>
+            <option value="tip5p">TIP5P (five-point model)</option>
         </param>
         <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/>