VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Sat Dec 12 2020 - 20:03:27 CST

This sounds trivial, but you don't note the answer, so I'll ask anyway. Did
you look at the individual dcd files that were being combined with catdcd,
for this particular set of trajectories? It is good to know whether the
unexpected behavior is caused by catdcd (exceedingly unlikely in this case)
or is present in your original trajectories.
Best,
Peter

On Sat, Dec 12, 2020 at 8:31 AM Kandarp Sojitra <sojitra_kandarp_at_iitgn.ac.in>
wrote:

> Hello,
>
> 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.
>
> Regards,
> Kandarp Sojitra
>
>