From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Aug 13 2012 - 21:11:20 CDT
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.
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