Re: "Jump" in Energy and Volume graphs of my MD

From: Peter Freddolino (
Date: Wed Mar 30 2016 - 15:23:46 CDT

Are you sure that on restart you are reading the extended system information from the restart file and not resetting the cell basis vectors?

> On Mar 30, 2016, at 4:04 PM, Daniela Rivas <> wrote:
> Dear NAMD 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!

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