Re: Analysis of FEP output file

From: Chris Chipot (Christophe.Chipot_at_edam.uhp-nancy.fr)
Date: Thu Feb 16 2012 - 07:35:12 CST

Dear Sudipta,

in all likelihood, you are using an outdated version of parseFEP. The
problem that you are seeing comes from the use of the Gaussian estimator
to measure your statistical error, which is appropriate only when your
probability distributions obey second-order perturbation theory. Originally,
we were computing the error both with a biased and an unbiased estimator,
which can yield the kind of problem that you are reporting when the
histograms have an appreciable skewness and kurtosity. In the latest
version of parseFEP, you can pick what you want. Though this version
is available in the CVS, I am attaching it herewith.

Best,

Chris Chipot

On 2/15/12 3:29 PM, Chris Harrison wrote:
> Dear Sudipta,
>
> This appears to be a problem involving the fep analysis tool in VMD.
> While I can't promise anything, you might have much better luck asking
> over on the vmd-l list about this particular problem.
> (www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/)
>
> Best,
> Chris
>
>
>
> On Tue, Jan 31, 2012 at 11:41 AM, sudipta<sudipta.mml_at_gmail.com> wrote:
>> Hi everyone,
>>
>> I want to perform FEP calculations using NAMD. Therefore, I have finished my
>> calculation according to tutorial and want to estimate the error of free
>> energy (BAR estimator) by using the parsefep plugin of VMD (v 1.9).
>> However, during this analysis, I am getting an error constantly that I
>> cannot resolve it. I put the error message below.
>>
>> Error: domain error: argument not in valid range.
>>
>> I have divided the whole path as
>>
>> runFEP 0.0 0.01 0.001 $numSteps
>> runFEP 0.01 0.1 0.01 $numSteps
>> runFEP 0.1 0.9 0.1 $numSteps
>> runFEP 0.9 0.99 0.01 $numSteps
>> runFEP 0.99 1.0 0.001 $numSteps
>>
>> for forward direction and
>>
>> runFEP 1.0 0.99 -0.001 $numSteps
>> runFEP 0.99 0.9 -0.01 $numSteps
>> runFEP 0.9 0.1 -0.1 $numSteps
>> runFEP 0.1 0.01 -0.01 $numSteps
>> runFEP 0.01 0.0 -0.001 $numSteps
>>
>> for backward direction
>> I have chosen the numSteps as 1500 and alchequilsteps as 500
>>
>> Insted of this above division, if I choose those as
>>
>> runFEP 0.0 0.1 0.001 $numSteps
>> runFEP 0.1 0.9 0.01 $numSteps
>> runFEP 0.9 1.0 0.001 $numSteps
>>
>> runFEP 1.0 0.9 -0.001 $numSteps
>> runFEP 0.9 0.1 -0.01 $numSteps
>> runFEP 0.1 0.0 -0.001 $numSteps
>>
>> for forward and backward direction then the calculations are finished
>> without any error. So, what is my wrong?
>>
>> Can anyone highlight in this regard.
>>
>> Thanks
>> Sudipta
>>
>> --
>> ==========================================================
>> Dr. Sudipta Kumar Sinha ||
>> Postdoctoral Employee ||
>> C/O Prof. Leonor Saiz ||
>> Department Of Biomedical Engineering ||
>> University of California, Davis ||
>> U.S.A ||
>> Email-sudipta.mml_at_gmail.com ||
>> ==========================================================
>>
>>
>
>

-- 
_______________________________________________________________________
Chris Chipot, Ph.D.
Équipe de dynamique des assemblages membranaires
Unité mixte de recherche CNRS/UHP No 7565
Université Henri Poincaré - Nancy 1           Phone: (33) 3-83-68-40-97
B.P. 239                                      Fax:   (33) 3-83-68-43-87
54506 Vandœuvre-lès-Nancy Cedex, France
                             E-mail: Christophe.Chipot_at_edam.uhp-nancy.fr
                                                      chipot_at_ks.uiuc.edu
                                            http://www.edam.uhp-nancy.fr
                                          http://www.ks.uiuc.edu/~chipot
       To sin by silence when we should protest makes cowards out of men
                                                     Ella Wheeler Wilcox
_______________________________________________________________________

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