Re: When using WHAM TO ANALYSIS

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Jun 27 2019 - 15:01:47 CDT

Hello Jiali, if you used a "width" of 1 (default) the force constant to be
used in WHAM is the same used for Colvars harmonic restraints. You just
need to check that the harmonic potential is defined the same way in the
WHAM implementation that you are using:
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvarbias_harmonic

If the results are not what you expect, this may be a sampling problem,
rather than a protocol error. Try computing and comparing PMFs on tiny
systems such as this one:
https://github.com/Colvars/examples/tree/master/tma-aco

Giacomo

On Thu, Jun 27, 2019 at 3:42 PM Jiali Wang <jwang204_at_binghamton.edu> wrote:

> Hi everyone,
> Good afternoon. I have a umbrella simulation under NAMD, when calculate
> in WHAM, I directly use constant where write in NAMD colvars, is that
> correct(I checked the email list, and suggest do it this way)? I found PMF
> energy is higher than I expect, and range about 60 to 110 Kcal/mol. Is that
> correct? and by increase the windows number, the PMF energy decreased, I
> didn't understand.
> I am confuse about how wham calculate PMF, is that relevant to colvartraj
> frequency? I found WHAM doesn't use frequency to calculate PMF
> thank you so much for your time!
> jiali
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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