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

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 31 18:36:04 CET 2011

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:


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.


> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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