[gmx-users] Using newly defined residue to neutralize the system

Justin Lemkul jalemkul at vt.edu
Wed Jan 18 18:37:21 CET 2017

On 1/18/17 3:04 AM, Sajeewa Pemasinghe wrote:
> Hi all,
> I have an itp file to a new residue MGH. It is an ion with a (+2) charge. I
> have included the itp file in the topology file using #include MGH.itp. My
> question is, will I be able to use this MGH ion to neutralize my system
> using "gmx genion" without any further modifications to the forcefield
> files? If there are further modifications needed could you please tell me
> what they are?

gmx genion will a monoatomic ion of whatever name you choose (-pname) and 
whatever charge (-pq).  The name you give should match whatever is in MGH.itp.



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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