[gmx-users] Question regarding the minimization of the system

[Justin Lemkul]

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

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================