[gmx-users] Problem related to solvating CNT and then removing out the molecules inside CNT

Justin Lemkul jalemkul at vt.edu
Sun Jul 13 18:40:58 CEST 2014

On 7/13/14, 12:31 PM, vivek sinha wrote:
> What changes in topology file should I do? Just the number of water
> molecules?

Yes.  If you removed waters, that must be reflected in the number of molecules 
listed in the topology.

> But I have also changed the atom number of each molecule while removing the
> molecules from inside.
> In other words my new .gro file also has the atom numbers in increasing
> order with no gap.

grompp doesn't care about the numbering in the .gro file.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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