From: John Stone (
Date: Thu Mar 31 2016 - 10:32:34 CDT

  I seem to vaguely recall that for some MD simulation configs, unless
you have velocity information saved/restored on restart (and appropriate
sim config flags perhaps), that atom velocities will be reinitialized
(using random number generators) which may explain such a bump upon restart.
This is really a question for NAMD-L or the mailing list for whichever
MD simulation code you happen to be using.

  John Stone

On Wed, Mar 30, 2016 at 05:01:39PM -0300, Daniela Rivas wrote:
> Dear VMD users,
> When analyzing the basic data (T, P, V, Energy and protein RMSD) of my MD
> I found that there was a "jump" in my Volume and Potential Energy graphs.
> This jump occurs just when I had to stop the simulation and re-started it
> from the restart files from the last step. I used all the restart files to
> re-start my simulation, and there's no problem with the Temperature,
> Pressure, Kinetic Energy or protein RMSD. Any thoughts of what could have
> happened? Has anyone else had this problem when restarting a MD?
> I hope you can help me solve this riddle. Thanks in advance!
> Daniela.

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349