[gmx-users] centering molecule for movies

Neha Gandhi n.gandhiau at gmail.com
Mon Jul 7 14:42:37 CEST 2014

Hi List,

I have simulated peptides in explicit water to form aggregate. I tried
various options to post-process my trajectory (after removing water) using
Gromacs 4.6.3 as described below. I want to record movie using VMD but the
molecule translates and rotates during movie hence, I cannot capture all
screen shots properly.

trjconv -f md.xtc -pbc mol -o x.xtc -s md.tpr -n index.ndx
trjconv -f x.xtc -ur compact -center -s md.tpr -n index.ndx

How do I keep the peptides in center to record the movie? Is it a vmd
problem or post-processing issue will fix it? If anybody has faced similar
issue and has found a solution, i would appreciate your help.

Many thanks,

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