[gmx-users] (no subject)

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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