From: Grace Brannigan (grace.brannigan_at_rutgers.edu)
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.
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2009-2010/0250.html
or
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2008-2009/4112.html
My guess is that you will dramatically reduce noise if you post process at
almost 0 degrees.
cheers,
Grace
On Mon, Aug 13, 2012 at 10:11 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> Does anyone have experience post-processing trajectories to get pressure
> profiles? I see here (
> http://www.ks.uiuc.edu/Research/namd/2.9/ug/node75.html ) 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 (856)225-6780 www.branniganlab.org
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