VMD-L Mailing List

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Mon Nov 30 2009 - 04:19:43 CST

Hi VMD users,

I had to kill a NAMD simulation before completion as our cluster had to be
shut down. My restart frequency being 1, I could restart later from the end
point with the restart.vel, restart.coor and restart.xsc files. However, the
.xsc file for the full trajectory (as much as it could run) is not written
down.

Now, I am interested in running NAMDenergy, and do need the .xsc file for
calculating some energies for my periodic system. The GUI version allows one
to write an .xsc if one is not available. Is there a way to do this in the
command line version of NAMDenergy (or maybe a more general way of writing
it, without even resorting to NAMDenergy)?

Also, I guess NAMDenergy writes the .xsc using the cell information at each
step in the .dcd (assuming the .dcd contained the unit cell information).
Please correct me if I am wrong here...

Thanks!
-Neela