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/gm
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
using WHAM based on
the data set on umbrella sampling.
Sanku
From: Laura Kingsley
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 PM
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
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
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