From: Chris Chipot (chipot_at_ks.uiuc.edu)
Date: Wed Oct 05 2011 - 01:10:24 CDT
Bruno,
the error that you are reporting can be ascribed to the calculation
of the statistical error based on both the standard FEP estimator
and the Gaussian estimator, which should be preferred when your
probability distributions are nearly Gaussian (see JPC B 2010, 114,
10235). If such is not the case, this estimator ought to be avoided.
We will correct this and let the user turn this option on when needed.
Chris Chipot
On 10/4/11 2:29 PM, Bruno Luís Pinto de Oliveira wrote:
> Thanks Chris and Jerome for your reply,
>
> > The data you are plotting is relative free energy: it is defined up to
> > an additive constant. The best way to represent the change along the
> > forward-and-backward simulation is to shift the backward curve by a
> > constant, so that the initial value (at lambda = 1) is the same free
> > energy as the final value from the forward run.
>
> I corrected the backward curve by subtracting the free energy obtained
> for lambda =1 in the foward calculation.
>
> Please find the graphic published here:
>
> http://www.boliveira.com/NAMD.html
>
> I'm not familiar enough with the FEP to see if the result is acceptable...
>
> I guess it is not so bad ...
>
> or Do I have to do longer simulations ???
>
> I tried to analyse the FEP calculations with the ParseFEP plugin as
> suggested by Chris Chipot however I am getting this error:
>
> domain error: argument not in valid range
> domain error: argument not in valid range
> while executing
> "expr sqrt($instant_error_gauss) "
> (procedure "::ParseFEP::FEP_formula" line 361)
> invoked from within
> "::ParseFEP::FEP_formula $file $file_entropy $file_lambda $window
> $mean_xi $fororback"
> (procedure "::ParseFEP::normal_parse_log" line 60)
> invoked from within
> "::ParseFEP::normal_parse_log $::ParseFEP::fepofile forward "
> (procedure "::ParseFEP::namdparse" line 172)
> invoked from within
> "::ParseFEP::namdparse"
> (in namespace inscope "::ParseFEP" script line 21)
> invoked from within
> "::namespace inscope ::ParseFEP {
> ##if {$::ParseFEP::fepbofile != ""} {set ::ParseFEP::sosindex 1 }
>
> if { [string length $fepofile] < 1 } {
> tk_dial..."
> invoked from within
> ".parseFEP.runbutton invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 24)
> invoked from within
> "tk::ButtonUp .parseFEP.runbutton"
> (command bound to event)
>
> I found this error reported in a previous message posted in the
> mailling list.
>
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/17776.html
>
> It seems that this error is related with some bug in parseFEP...
>
> However it is strange because I have instaled the last version of VMD
> (VMD 1.9 Windows OpenGL, CUDA (Windows XP/Vista/7 (32-bit) with OpenGL
> and CUDA).
>
> Can someone confirm if this error is related with some bug or if I am
> doing something wrong???
>
> Tkanks you in advance
>
> Bruno
>
>
> >> Dear all,
> >>
> >> I am new to FEP and since the last months I have gotten great help
> from the
> >> mailing list. Thanks to all who help me...
> >>
> >> I am posting this message because I have a new doubt about the reverse
> >> calculation to
> >> monitor the hysteresis.
> >>
> >> Briefly, I would like to estimate the difference in the binding energy
> >> between a Rhenium complex and the corresponding ligand (compounds are
> >> exactly the same with the exception that the ligand lacks the
> metallic part
> >> Re(CO)3; the Re(CO)3 vanish).
> >>
> >> I did the foward transformation (transformation in water and
> protein; lambda
> >> goes from 0 to 1) and the calculated results are in good agreement
> with the
> >> experimental results (I used a thermodynamic cycle that someone in a
> >> previous post confirmed that is correct; I am using 16 ps of
> equilibration
> >> and 80 ps of colection per lambda, 32 states, ~3ns).
> >>
> >> Then, I used the end of the foward transformation as the starting
> point for
> >> the reverse simulation (lambda goes from 1 to 0).
> >>
> >> For example, the transformation of the Rhenium complex into the
> ligand gave
> >> -31.33 kcal/mol (forward) and 35.34 kcal/mol (backward).
> >> From the literature that I read I realized that the backward
> transformation
> >> should display more or less the same free energy change of the forward
> >> transformation but with an opposite sign. Did I understood well?
> >>
> >> if so can I assume that the hysteresis is acceptable???
> >>
> >> or I need to plot the DG against the lambda as examplified in the
> tutorial
> >> of Christophe Chipot et al.
> >>
> >> I did it and as you can see in the graphic the foward and backward
> curves do
> >> not converge.
> >>
> >> http://www.boliveira.com/NAMD.html
> >>
> >> I am confuse because if the values of the backward and foward
> transformation
> >> should have opposite sign of course they will never converge.
> >>
> >> I feel that I'm missing some step but I can not figure out what...
> >>
> >> Excuse me the long post but all my group works with amber/TI and I
> dont have
> >> anyone who can help me.
> >>
> >> Can anyone help me in all these doubts??
> >>
> >> Any help is highly appreciated...
> >>
> >> Thanks in advance
> >>
> >> Bruno
> >>
> >>
>
>
> --
> _______________________________________________________________________
>
> Chris Chipot, Ph.D.
> Theoretical and Computational Biophysics Group
> Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 North Mathews Phone: (217) 244-5711
> Urbana, Illinois 61801 Fax: (217) 244-6078
>
> E-mail: chipot_at_ks.uiuc.edu
> Christophe.Chipot_at_edam.uhp-nancy.fr
> Web: http://www.ks.uiuc.edu/~chipot
> http://www.edam.uhp-nancy.fr
>
> The light shines in the darkness, and the darkness has not overcome it.
> John 1:5.
> _______________________________________________________________________
>
--
_______________________________________________________________________
Chris Chipot, Ph.D.
Theoretical and Computational Biophysics Group
Beckman Institute
University of Illinois at Urbana-Champaign
405 North Mathews Phone: (217) 244-5711
Urbana, Illinois 61801 Fax: (217) 244-6078
E-mail: chipot_at_ks.uiuc.edu
Christophe.Chipot_at_edam.uhp-nancy.fr
Web: http://www.ks.uiuc.edu/~chipot
http://www.edam.uhp-nancy.fr
The light shines in the darkness, and the darkness has not overcome it.
John 1:5.
_______________________________________________________________________
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