From: Grace Brannigan (grace.brannigan_at_rutgers.edu)
Date: Mon Aug 20 2012 - 11:22:12 CDT
We post-processed the trajectories using the procedure you describe - one
run for Ewald and one run for everything else, then added them together. We
used the exact same configuration as for the run, (with the exception of
the temperature) - and set the values of pressureProfileEwaldX,Y,Z to
correspond to those of the PME in the simulation.
We didn't get big fluctuations with T ~ 0, but we analyzed thousands of
frames - I guess you have far fewer? We did find that with T~0 increasing
the number of frames improved the situation far more than with T~300K. If
the overall group pressure (i.e. the trace of the pressure tensor, output
on-the-fly) isn't converged over the number of frames you have then yeah, I
agree that it's unlikely the individual components will be converged,
regardless of how you set the temperature in post-processing.
On Sat, Aug 18, 2012 at 7:24 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> Sorry for taking so long to reply, but I've been running a battery
> of tests to try to get to the bottom of this.
> I had seen your previous post and was hoping you would chime in. The
> problem here is that I want the actual pressure profiles, not the surface
> tension (I was just trying that as a check, and I did try it as well with T
> = 0). So I can't just ignore the kinetic term.
> I ran my tests on a water box, calculating the profiles both during and
> post-processing. Through trial and error, I determined that the proper
> approach for post-processing is to run two calculations, both with the
> exact same configuration as the simulation itself (including both runs
> using PME), one to get all the contributions except for the Ewald part and
> one just to get Ewald. An important point I figured out here: the value
> of pressureProfileEwaldX,Y,Z really matters. When I used 20, it was much
> slower, but gave different results than 10. I tried 40, which is extremely
> slow, but is almost the same as 20, suggesting that using a value of 20
> ensures this quantity is converged.
> I also ran a test for 100 steps, getting the pressures and the profiles
> with 1 slab every step. From this I was able to confirm what I found
> above. The sum of the concurrently run profile and the Ewald component
> with "pPEX,Y,Z 20" gives precisely the same value as the group pressure
> determined by NAMD. Post-processed (therefore with a different kinetic
> term) was similar, but with a small deviation as expected.
> Ultimately, what I'm concluding here is that the noise is primarily due to
> the fluctuations in the pressure calculations, not the kinetic term. Even
> at T=0 and a single slab, the fluctuations in the pressure profiles for the
> water box (and thus also the surface tension) are +/- 160 bars. So the
> profiles are not reliable, at least for so few samples, which is all I have
> from the DCDs.
> So Grace, when you did your calculations, did you 1) post-process the
> trajectories and 2) see similar fluctuations, even at T=0?
> On Aug 16, 2012, at 2:33 PM, Grace Brannigan wrote:
> 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 <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.
> Grace Brannigan
> Assistant Professor
> Center for Computational and Integrative Biology (CCIB) &
> Department of Physics
> Rutgers University, Camden, NJ
-- 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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