[gmx-users] PROTEIN FOLDING

[Justin Lemkul]

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

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

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jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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