[gmx-users] Jarzinsky's inequality from SMD simulation

[Justin A. Lemkul]

Laura Kingsley wrote:
> Yes, I believe that is correct. I know that this is one way to get the 
> PMF using Gromacs. I am not sure if there is a way to use the Jarzinsky 
> equation explicitly to extract the PMF from just a sMD run with Gromacs.
> 

One approach:

http://lists.gromacs.org/pipermail/gmx-users/2011-August/063477.html

I've never tried it, so I don't know if that is correct or not.  Go to 
http://www.gromacs.org/Support/Mailing_Lists/Search and search for "Jarzynski" 
and you will pull up more on this topic.

-Justin

> On 10/31/2011 01:29 PM, Sanku M wrote:
>> using SMD simulation. What is does that it uses SMD to generate the 
>> initial configurations for different windows and then perform umbrella 
>> sampling separately on each windows to subsequently extract the PMF 
>> using WHAM based on the data set on umbrella sampling.
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================