From: Chris Harrison (charris5_at_gmail.com)
Date: Thu May 03 2012 - 18:42:19 CDT
Yes. However, in the limit of converged sampling the Langevin forces are
theoretically canceling out to noise. ....theoretically. In practice, it
is entirely possible that when using a Langevin thermostat you might see
the periodicity produced from the kicks when analyzing the forces.
"Will the Langevin forces affect PMF calculations?" That entirely depends
on the PMF you are performing. Many considerations go into answering that
question. Consider: Are the forces being predominately measured in the PMF
of a small enough scale that the Langevin kicks can be resolved? If
performed correctly, the Langevin forces should look like noise. Another
consideration: a purist would argue to perform an NVE simulation, removing
as many external forces/perturbations from the system as possible.
Unfortunately the answer to your question is: yes, they can affect PMFs,
but a) will it matter for the question you are asking, and b) you will have
to test to actually determine for sure; or alternatively pursue an NVE
ensemble simulation.
Best,
Chris
On Thu, May 3, 2012 at 3:43 PM, Xiaohu Li <xiaohu-li_at_northwestern.edu>wrote:
> Dear NAMD users,
> I have a question regarding the forces saved in forcedcd file.
> suppose I'm doing NVT using Langevin dynamics, will the forces saved in
> forcedcd contain the random forces from Langevin dynamics?
> Do those random forces affect, say, PMF calculations if they are
> included?
> Thanks.
>
>
-- Chris Harrison, Ph.D. NIH Center for Macromolecular Modeling and Bioinformatics Theoretical and Computational Biophysics Group Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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