From: Chris Chipot (chipot_at_ks.uiuc.edu)
Date: Mon Oct 03 2011 - 07:05:16 CDT
Bruno,
if I may add something to Jerome's reply, this is all taken care of in
the VMD
plugin ParseFEP, which is designed for the analysis of FEP calculations.
Cheers,
Chris Chipot
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.
>
> Cheers,
> Jerome
>
> 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.
>>
>> 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.
_______________________________________________________________________
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