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From: Yan Li <liyantiger.yahoo.com>

Date: Wed, 8 Aug 2012 18:43:02 -0700 (PDT)

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
*

*>
*

Date: Wed, 8 Aug 2012 18:43:02 -0700 (PDT)

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,

-- ================================ 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/amberReceived on Wed Aug 08 2012 - 19:00:02 PDT

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