Laura Kingsley wrote:
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.
One approach:
http://lists.gromacs.org/pipermail/gmx-users/2011-August/063477.html
I've never tried it, so I don't know if that is correct or not. Go to
http://www.gromacs.org/Support/Mailing_Lists/Search and search for "Jarzynski"
and you will pull up more on this topic.
-Justin
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.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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