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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