[gmx-users] How to center my trimer in my simulation box.

Ilya Chorny ichorny at gmail.com
Tue Apr 22 23:14:19 CEST 2008


I am simulating a trimer in a membrane. In one of my simulation  two of the
monomers are on one side of the box and the other monomer is on the other
side of the box. I tried using trjconv to center the whole thing in the
center of my simulation cell but have failed miserably. I also searched
around for about an hour and could not find anything.

I use trjconv -f *.gro -s *.tpr -center rect -pbc whole -o *.gro.

Any advice?



Ilya Chorny Ph.D.
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