[gmx-users] Adding Urea in simulation

Justin Lemkul jalemkul at vt.edu
Wed Mar 5 12:12:59 CET 2014

On 3/5/14, 5:58 AM, bharat gupta wrote:
> Hi,
> 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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