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

Sanku M msanku65 at yahoo.com
Mon Oct 31 18:29:53 CET 2011

Hi Laura,
  I do not think Justin Lemkul's tutorial is suggesting extracting PMF 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.


From: Laura Kingsley <lkingsle at purdue.edu>
To: gmx-users at gromacs.org
Sent: Monday, October 31, 2011 11:09 AM
Subject: Re: [gmx-users] Jarzinsky's inequality from SMD simulation

There is a way to extract the PMF from sMD simulations using the weighted histogram analysis method (WHAM) in gromacs- Justin Lemkul's tutorial does a nice job of explaining it:


- Laura

On 10/31/2011 11:05 AM, Sanku M wrote: 
>  I have done some steered MD simulation and I want to construct the potential of mean force from these pull-profile using Jarzinsky's inequality. I wanted to see whether, in updated version of gromacs, there is any implementation of  extracting PMF from SMD simulations. 
>If not, can anyone suggest some guidelines how to do it.

Laura Kingsley Graduate Student
Medicinal Chemistry and Molecular Pharmacology
Purdue University 
Office: RHPH 504A 
575 Stadium Mall Dr.
West Lafayette, IN 47907
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