[gmx-users] Your solvent group size (*) is not a multiple of *
jalemkul at vt.edu
Tue Dec 9 15:29:06 CET 2014
On 12/9/14 9:25 AM, Hassan Aaryapour wrote:
> Dear Gromacs Users,
> I'm new in gromacs and I have been trying to add ions to the simulation box
> using following command in gromacs 5:
> gmx genion -s ions.tpr -o conf-ion.pdb -p topol.top -neutral -conc 0.15
> then I selected these groups(Protein, MG, Ligand, respectively): 1 | 13 |
> This error was appeared:
> Program gmx, VERSION 5.0
> Source code file:
> /home/QMMM/ProgramFiles/gromacs-5.0/src/gromacs/gmxana/gmx_genion.c, line:
> Fatal error:
> Your solvent group size (2701) is not a multiple of 9
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> I found this URL "
> http://comments.gmane.org/gmane.science.biology.gromacs.user/64577" in
> related to my question but i don't understand answer to resolve my error?
> Indeed, I 've already successfully simulated another protein with same
> gromacs and commands.
You shouldn't be replacing a merged group of protein, Mg, and ligand with ions.
You need to choose some sort of solvent (water) with ions. This requires no
custom group to do.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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