[gmx-users] Adding Urea in simulation
bharat.85.monu at gmail.com
Wed Mar 5 13:11:17 CET 2014
Thanks Justin ... The problem was with the memory .. I ran the same
calculation on separate system and I worked perfectly fine ...
On Wed, Mar 5, 2014 at 8:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
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> 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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