From: Kandarp Sojitra (
Date: Sat Dec 12 2020 - 06:36:45 CST


I am working on MD simulation of proteins. One of my systems had a few
number of dcd files, which I concatenated using catdcd. After concatenating
when I load the psf and dcd in VMD and play all the frames I am observing
the protein to be fixed at a point while the water box keeps on moving. As
far as I understand when we provide PBC the water box should remain fixed
while protein can move around. I have observed this discrepancy for only
one system, while for other concatenated trajectories I am observing the
correct trend.
I have checked my config, coordinates and structure files and it looks
fine. It is the same as I usually run, where I have never observed this
problem. So could you please explain what could be wrong with this or where
could I have been making some mistakes?
Thank you very much in advance.

Kandarp Sojitra