VMD-L Mailing List

From: _at_huji.ac.il
Date: Tue Dec 26 2006 - 04:54:20 CST

Dear VMD developers
I'm trying to find some function that allows to recenter my peptide in a
PBC every couple of frames during the simulation. I want to be able to
preclude center of mass motion due to external forces as random noise in
Langevin dynamics. Another option is to use VMD in order be able to
recenter the peptide in PBC after minimization in the trajectory. I
know that this question has appeared once. I tried the answers but it
didn't work. I tried to use ptraj program. It puts the peptide in the
center (0,0,0) but not at the center of my PBC. Anyone who knows,
please, answer. Looking for your answer as soon as possible. Thank you
very much for your help
Regina