[gmx-users] grompp erros

Justin Lemkul jalemkul at vt.edu
Wed Jul 2 13:59:55 CEST 2014

On 7/2/14, 5:39 AM, Linlin Sun wrote:
> Hello everyone,
> In order to build a virtual site which is independent from other structure,
> I have created a new atom type and set the mass of this new atom type to
> zero. However, when I use* grompp*, it failed with fatal errors, which
> complain about the zero mass of the new atom type.
> Anyone could possibly know how to get around this problem? Any suggestions
> would be helpful. Thanks very much!

If you've declared it as an atom (particle type "A"), then that's probably why 
you're getting this error.  Virtual site types are particle type "V" in 
ffnonbonded.itp.  I guess the larger point is - why have a virtual site that is 
not dependent upon any other elements of the structure?



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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