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.
Sanku
________________________________
From: Laura Kingsley <lking...@purdue.edu>
To: gmx-users@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:
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
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Laura Kingsley Graduate Student
Medicinal Chemistry and Molecular Pharmacology
Purdue University
Office: RHPH 504A
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