From: Chris Chipot (chipot_at_ks.uiuc.edu)
Date: Mon Oct 03 2011 - 07:05:16 CDT
if I may add something to Jerome's reply, this is all taken care of in
plugin ParseFEP, which is designed for the analysis of FEP calculations.
On 10/3/11 6:49 AM, Jérôme Hénin wrote:
> Hi Bruno,
> 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.
> 2011/10/3 Bruno Luís Pinto de Oliveira<boliveira_at_itn.pt>:
>> 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.
>> 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
-- _______________________________________________________________________ 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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