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From: Daniel Sindhikara <sindhikara.gmail.com>

Date: Fri, 10 Aug 2012 10:40:00 +0900

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
*

*> radak004.umn.edu :
*

*> radakb.biomaps.rutgers.edu
*

*> ====================================================================
*

*> Sorry for the multiple e-mail addresses, just use the institute
*

*> appropriate address.
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

Date: Fri, 10 Aug 2012 10:40:00 +0900

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:

-- 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> -- _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Aug 09 2012 - 19:00:03 PDT

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