Mercurial > repos > chemteam > gmx_em

diff minim.xml @ 2:0725fe83f0df draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
author chemteam
date Thu, 28 Mar 2019 10:06:31 -0400
parents 3158b8b4e981
children 1f3eb6cea5ba
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line diff
--- a/minim.xml	Thu Oct 04 18:17:26 2018 -0400
+++ b/minim.xml	Thu Mar 28 10:06:31 2019 -0400
@@ -17,7 +17,7 @@
         ln -s '$gro_input' ./solv_ions.gro &&
         ln -s '$top_input' ./top_input.top &&
   
-        gmx grompp -f ./minim.mdp -c ./solv_ions.gro -p ./top_input.top -o em.tpr &>> verbose.txt &&
+        gmx grompp -f ./minim.mdp -c ./solv_ions.gro -r ./solv_ions.gro -p ./top_input.top -o em.tpr &>> verbose.txt &&
         gmx mdrun -deffnm em &>> verbose.txt
         
     ]]></command>
@@ -115,7 +115,7 @@
     </tests>
     <help><![CDATA[
 
-Upload GRO and TOP files for energy minimisation. To take advantage of all GROMACS features, upload an MDP file with simulation parameters. Otherwise, choose parameters through the Galaxy interface. See http://manual.gromacs.org/online/mdp_opt.html for more information on the options.
+Upload GRO and TOP files for energy minimisation. To take advantage of all GROMACS features, upload an MDP file with simulation parameters. Otherwise, choose parameters through the Galaxy interface. See http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html for more information on the options.
 
     ]]></help>