Re: pressure profile calculations

From: Grace Brannigan (
Date: Thu Aug 16 2012 - 14:33:21 CDT

Hi JC,

I found that most of the noise in the pressure profiles was due to the
ideal gas term, which is artificially noisy in post processing because
velocities are randomly reassigned - see e.g.


My guess is that you will dramatically reduce noise if you post process at
almost 0 degrees.


On Mon, Aug 13, 2012 at 10:11 PM, JC Gumbart <> wrote:

> Does anyone have experience post-processing trajectories to get pressure
> profiles? I see here (
> ) that I need to
> do separate calculations for the non-Ewald and Ewald contributions. One
> thing that is not obvious to me though is if I should turn off PME for the
> non-Ewald offline run. I would guess it should be left on, as one might
> typically calculate the non-Ewald component during the simulation itself,
> in which PME was on. Nonetheless, this assumption may or may not be valid.
> A bigger question though - given the large fluctuations in pressure, how
> useful is a completely offline calculation? Because I only saved my
> trajectory every 1000 timesteps, for a 1 ns run, I have only 1000 frames
> from which to calculate and average the profiles. So they are quite noisy.
> But more importantly, the surface tension does not approach 0 at the edges
> of my profile, but it does appear to level off to something (modulo the
> large fluctuations anyway). Maybe this is just due to insufficient
> sampling of the pressure, or maybe I'm doing something completely wrong?
> If anyone has done these calculations and gotten results that seem
> reasonable, please chime in with precisely how you did them.
> Thanks!
> JC

Grace Brannigan
Assistant Professor
Center for Computational and Integrative Biology (CCIB) &
Department of Physics
Rutgers University, Camden, NJ

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:55 CST