[gmx-users] (no subject)

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 11 12:15:21 CEST 2012

On 7/11/12 6:00 AM, amir abbasi wrote:
> Hi All!
> I want to use Implicit solvent to simulate a nucleic acid sequence.
> How can I do it?
> I use this command:
> genion -s ions.tpr -o nucleic_ions.gro -p nucleic.top -pname K+ -nname
> CL -neutral -conc 0.1
> ions.tpr file is same as umbrella sampling tutorial.
> I got this error message:
> Fatal error:
> Your solvent group size (2898) is not a multiple of 31
> what should I do?

One does not typically add explicit ions in an implicit solvent system.  genion 
fails because it appears you are trying to replace parts of your nucleic acid 
with ions.



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


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