[gmx-users] output file format under pbc

Justin Lemkul jalemkul at vt.edu
Fri Aug 26 13:47:46 CEST 2016

On 8/25/16 11:36 PM, Chang Woon Jang wrote:
> Dear Gromacs Users,
>   I would like to describe the situation. An initial molecule in the
> periodic boundary condition is located near the right side of box. The box
> is big, thus needs to be adjusted and equilibrated under NPT. The box
> should be shrinked after few ns seconds. The molecule near the right side
> of box during the simulation is moving to the right and some of atoms of
> the molecule would appearing the left side of box.
>   In this configuration, the molecule looks separated but actually
> connected because of PBC. However, I want the molecule as an initial
> continuous single molecule in the* "adjusted equilibrated box" *for the
> next run. Yes, it is the equilibrated shrinked box.
>    Can this be solved by "trjconv" or something else?

Have you tried?  The main purpose of trjconv is to correct for PBC effects.



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 mailing list