[gmx-users] Jarzinsky's inequality from SMD simulation
lkingsle at purdue.edu
Mon Oct 31 16:09:01 CET 2011
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:
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.
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