From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Mon Oct 03 2011 - 06:49:46 CDT
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
>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:48 CST