From: Grace Brannigan (grace.brannigan_at_rutgers.edu)
Date: Fri Aug 17 2012 - 06:16:21 CDT
Hi,
Just wanted to add a quick p.s. - it is straightforward to tell if the
noise is artificially introduced during postprocessing by simply running
the postprocessing twice and seeing if you get significantly different
results. It seems like an ideal solution to this problem would be to use a
velocity dcd file rather than having velocities regenerated in every frame
of the postprocessing, but I think an alternate reasonable solution is to
simply assume that velocities are isotropic on average. This is
effectively what you are doing if you set the temperature to (almost 0) in
the postprocessing run.
cheers,
Grace
On Thu, Aug 16, 2012 at 3:33 PM, Grace Brannigan <
grace.brannigan_at_rutgers.edu> 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.
>
>
> 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
>
>
-- 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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