Re: Question about "Free Energy of Conformational Change Calculations"

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Feb 06 2012 - 11:13:21 CST

Hello Han, the feature you're using is being discontinued, as stated on the
user's guide. The collective variables module gives you more options to
perform PMF calculations. For example, you may start with the ABF
tutorial, and then look at the user's guide. The tutorial is essentially
an example, and does not replace the full documentation.

Secondly, plan to simulate much longer than 100 ps if you want the free
energy of association of two protein monomers!!!

Giacomo

On Mon, Feb 6, 2012 at 12:03 PM, Shen, Han <han.shen_at_bme.gatech.edu> wrote:

> Dear All,
>
> I tried to follow "Free Energy of Conformational Change Calculations" to
> calculate the free energy of dimer separation. During the simulation, I
> separate the dimer from 5A to 30A, and then move them back to 5A. The pmf
> file is as below.
>
> pmf {
> task = grow
> time = 1 ps
> print = 1 ps
> }
>
> pmf {
> task = up ## move from 5A to 30A
> time = 100 ps
> }
>
> pmf {
> task = down ## move from 30A to 5A
> time = 100 ps
> }
> }
>
> However, the free energy at the beginning of "down" is not the same as the
> end of "up", looks like that it has been reset. Both the free energy of
> "down" and "up" keep growing during the task, which doesn't look like the
> real case. I am not sure if I did something wrong or this is not the proper
> method for my study. Is there a tutorial for this method? Hope someone can
> give me some suggestions! Thanks so much in advance!
>
> --
> Han Shen
> Wallace H. Coulter Department of Biomedical Engineering
> Georgia Institute of Technology and Emory University
>
>

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