[gmx-users] Adding Urea in simulation
jalemkul at vt.edu
Wed Mar 5 12:12:59 CET 2014
On 3/5/14, 5:58 AM, bharat gupta wrote:
> I am trying to add 5M urea in a box of volume 1453.73 cubic nm, which is
> equal to 4377 molecules of urea. But while adding it using genbox command,
> I get an error "killed" and the program stops after that. What is wrong
> here, is my calculation correct or the size of box should need to be
> increased ??
Without your actual command(s), there's little to suggest. genbox is running
out of memory trying to do whatever you've asked. Try with the 5.0-beta program
insert-molecules; IIRC some memory leaks have been fixed and it is more efficient.
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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