[gmx-users] Adding ions

[Amir Marcovitz]

Hi,

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
topol.top

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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