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.
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.
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Purdue University
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