[gmx-users] Question regarding the minimization of the system
jalemkul at vt.edu
Sat Feb 18 23:15:39 CET 2017
On 2/18/17 2:42 PM, ali.khourshaei71 at student.sharif.edu wrote:
> Dear Gromacs users,
> During surfing the Internet, I found a Draft of an paper. Within it, for
> minimization of lipid bilayer system, they first remove the periodicity
> by the use of trjconv and then use mdrun to minimize it. I think it's
> false. But, I just want to make sure of it.
mdrun doesn't care if molecules are whole or not. The .tpr has topology
information, so connectivity is known and the physics is carried out correctly
regardless of our visualization convenience.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
More information about the gromacs.org_gmx-users