Re: Re: When using WHAM TO ANALYSIS

From: Jiali Wang (jwang204_at_binghamton.edu)
Date: Thu Jun 27 2019 - 15:10:40 CDT

Thank you for your help! I will try it.
Jiali

On Thu, Jun 27, 2019 at 4:06 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> 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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