[gmx-users] Adding ions

Andrea Muntean andreamuntean at gmail.com
Wed Nov 18 12:25:49 CET 2009

The problem I was facing earlier: in the force field files (I am ussing
ffG53a6) the ions are named NA+, CL-, for example, so with capital letters.
Genion will add to the topology the ions named by default Na or Cl, unless
you use the options -pname and/or -nname to name the ions. I do so and I
have no mismatch of ionsname in different files. I hope this helps.


2009/11/17 Arden Perkins <perkina2 at eou.edu>

> 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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