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

[Laura Kingsley]

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:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html

- Laura



On 10/31/2011 11:05 AM, Sanku M wrote:
> Hi,
>   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.
> Sanku

-- 
Laura Kingsley

Graduate Student
Medicinal Chemistry and Molecular Pharmacology
Purdue University
Office: RHPH 504A
575 Stadium Mall Dr.
West Lafayette, IN 47907
Office Phone: (765) 496-6643

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