Justin Lemkul jalemkul at vt.edu
Sat Dec 30 17:13:12 CET 2017

On 12/30/17 10:47 AM, Alexandr Nasedkin wrote:
> gmx trjconv -s prd.tpr -f trajwhole.xtc -pbc nojump -o trajclust.xtc 
> -n index.ndx -center

Removing jumps and centering simultaneously should be considered 
mutually exclusive. One usually needs a few rounds of trjconv, e.g.

gmx trjconv -pbc whole
gmx trjconv -pbc nojump
gmx trjconv -pbc mol -center

Almost always does the trick for simple systems.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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