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

Laura Kingsley lkingsle at purdue.edu
Mon Oct 31 18:33:20 CET 2011

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.

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.

Laura Kingsley

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