[gmx-users] Adding ions

Amir Marcovitz amarcovitz at gmail.com
Thu Nov 19 10:57:21 CET 2009


Make sure you do specify the explicit names of the topology and structure
file. in the mannual they omit the suffix of the file.
for the purpose of rigourism -  this is the line i'm using:

        genion -pname Na+ -nname Cl- -o file_ionized.gro  -conc  0.2  -p

On Tue, Nov 17, 2009 at 1:56 AM, Arden Perkins <perkina2 at eou.edu> wrote:

> I am an undergraduate student and I am still learning to use GROMACS. When
> I add my ions to the solution (using genion) by the procedure described in
> the funnel web spider tutorial the .gro and .top files do not match. I tried
> subtracting solvent molecules but they still dont match and I can't
> continue. What am I doing wrong?
> Thanks!
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