[gmx-users] Adding ions

Justin A. Lemkul jalemkul at vt.edu
Tue Nov 17 01:05:31 CET 2009

Arden Perkins 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?

Hard to say.  The bottom line is you haven't updated the topology correctly.  If 
you use the -p flag with genbox (when adding solvent) and genion (when adding 
ions) the changes are made automatically and you don't have to worry about 
troubleshooting :)

For information on the error:



> Thanks!


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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