[gmx-users] System Charge

[Justin Lemkul]

On 6/10/17 10:08 AM, Quyen V. Vu wrote:
> Hi, you can calculate exactly the number of each atom types to add to the
> system by option -np -nn
> I also encounter problem with genion module when I try to add multivalent
> salt to my system ( e.g MgCl2) It treat Mg as monovalent and add to my
> system, then in grompp step, grompp prompt that my system is not neutral.
> In my opinion, your system must be neutral if you use PME to calculate
> coulomb potential
> 

If you're adding a divalent ion, then you need to tell genion of this fact using 
-pq.

-Justin

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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