[gmx-users] MD with splitted system

[Justin Lemkul]

On 4/3/14, 4:41 PM, davhak wrote:
> Dear All,
>
> After a minimization of a membrane bilayer system with Gromacs 4.6.4
> (charmm36 ff) the system got splitted into 4 parts in x/y plane (snapshot is
> attached). This was not noticed by me at that time (all previous
> minimizations ended without such splitting) and MD was started. The frames
> extracted with "trjconv -pbc res -ur compact" from MD trajectory of this
> system shows the membrane in a single piece with no splitting.
> Does this mean that Gromacs MD tolerates such a split system and take all
> the interactions as in an unslitted one so that one can assume that the MD
> is valid?
>

This is a normal consequence of periodicity when the system is centered at 
(0,0,0) rather than the box center, which is the normal Gromacs convention. 
Nothing is wrong; it's just inconvenient to look at.

-Justin

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

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

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