To add. This all depends on your WHAM program too. Most WHAM programs have
a certain formula for umbrella sampling. You need to make sure which
formula they use k_i(x-x_i)^2 or 1/2k_i(x-x_i)^2. If you use modular
reweighting software, you directly input the log of the biasing factor ->
ln(-U_umbrella/kT). This skips the need to interpret the formula of the
WHAM software (but as always, you need to know what the biasing potential
used in the simulation was).
-Dan
On Thu, Aug 9, 2012 at 10:43 AM, Yan Li <liyantiger.yahoo.com> wrote:
> Hi Brian,
>
> Thanks a lot for your reply.
>
> I think I come to understand how the spring constant is used in WHAM
> according to your explanation. I am going to test what WHAM will
> output when different spring constant values are given. I was just
> wondering whether it already was known. I completely agree with you that
> WHAM is not needed if I can sample without restraint.
>
> best wishes,
> Yan
>
>
> ________________________________
> From: Brian Radak <radak004.umn.edu>
> To: Yan Li <liyantiger.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
> Sent: Wednesday, August 8, 2012 3:11 PM
> Subject: Re: [AMBER] question about calculation of PMF with WHAM
>
>
> Hi Yan,
>
> 1.) The spring constant you need depends on whether or not you use the
> nmropt module or the ncsu_pmd module. What is actually needed in WHAM (and
> similar variants like MBAR) is the bias potential energy in all
> configurations and simulations; this is easily recomputed if the spring
> constants and bias anchor points are known and you have the bias coordinate
> timeseries saved.
>
> 2.) This question is interesting. I believe the answer is yes, but with
> some interesting qualifiers. Why don't you just try it? Playing with the
> WHAM equations would be useful too.
>
> 3.) If you can sample without any restraints, then you have no need for
> WHAM since the sampling weights are all unity in that case (although I'm
> not 100% a program will converge to this result). All you need to do in
> that case is generate an estimate of the probability density (probably a
> histogram) and take its negative logarithm (you could also integrate the
> mean force in that case too).
>
> Regards,
> Brian
>
>
> On Wed, Aug 8, 2012 at 1:07 PM, Yan Li <liyantiger.yahoo.com> wrote:
>
> Dear Amber users,
> >
> >I am trying to calculate PMF with WHAM, and have a question about the
> spring constant. In Amber manual, it says PMF can be computed using
> umbrella sampling. And in WHAM input file, the spring constant from
> umbrella sampling is needed. It looks the spring constant is necessary, but
> I wonder how the spring constant is used in WHAM after reading WHAM manual.
> >The first question is that, in many MD trajectories with umbrella
> sampling, if all time series data have the same spring constant, does the
> absolute value of the spring constant affect WHAM results? For example, if
> the spring constant is set to 2 or 4 in WHAM input file no matter what it
> is in MD, will it generate different energy surfaces?
> >Another question is that, suppose that I have a very long MD trajectory
> (long enough to sample) without any constraint, is it possible to calculate
> PMF from this trajectory? If possible, what should the spring constant be?
> >It looks like a stupid question. I would very appreciate that you could
> correct my misunderstanding. Thank you for your time.
> >
> >best wishes,
> >Yan
> >
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Center for
> Integrative Proteomics Room 308
> Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> Department of Chemistry : Piscataway, NJ
> 08854-8066
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> radakb.biomaps.rutgers.edu
> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute
> appropriate address.
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--
Dr. Daniel J. Sindhikara <http://www.dansindhikara.com/Information.html>
Ritsumeikan University <http://www.ritsumei.ac.jp/eng/>
sindhikara.gmail.com <http://www.dansindhikara.com>
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Received on Thu Aug 09 2012 - 19:00:03 PDT
