Vijayaraj wrote:
Message: 4
Date: Wed, 16 Nov 2011 09:34:02 -0500
From: "Justin A. Lemkul" <[email protected] <mailto:[email protected]>>
Subject: Re: [gmx-users] pulling force vs free energy
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
Message-ID: <[email protected] <mailto:[email protected]>>
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Vijayaraj wrote:
> Hi,
>
> What is the relation between pulling force and free energy of
binding.
> can we relate the maximum pulling force with the free energy. for
> example, 2 systems has the maximum pulling force and free energy as
> below from umbrella sampling and g_wham analysis,
>
> max. force free energy
> system 1 1470 42
> system 2 1647 32
>
> system 2 has higher pulling force than system 1 and the free energy
> result is different from this trend.
>
How did you obtain the maximum force, just a single SMD trajectory?
If so, I
wouldn't put a lot of faith in it necessarily. Umbrella sampling is
a more
robust method than a single pull. You can use large numbers of pulling
simulations and apply Jarzynski's equation to calculate free energy,
but there
are distinct caveats (although I suppose there are caveats with any
method).
-Justin
yes. the max force is obtained from single SMD trajectory. So in this
case we dont have to worry about the correction between max. force and
free energy. I found one of my free energy result is 2 times larger than
the previous result, where they have applied Jarzynski's equation.
SMD is path-dependent, while a true DeltaG is a path-independent quantity.
Hence why you cannot easily connect the two. Convergence in sampling and
limitations in each technique make it sometimes hard to compare the results that
others have obtained with other methods. Proper data collection for Jarzynski's
method requires exhaustive sampling, which is often hard to obtain (not a blind
criticism of others' work, just a fact).
-Justin
--
========================================
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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