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Message: 4<br>
Date: Wed, 16 Nov 2011 09:34:02 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] pulling force vs free energy<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4EC3C9DA.7040400@vt.edu">4EC3C9DA.7040400@vt.edu</a>><br>
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Vijayaraj wrote:<br>
> Hi,<br>
><br>
> What is the relation between pulling force and free energy of binding.<br>
> can we relate the maximum pulling force with the free energy. for<br>
> example, 2 systems has the maximum pulling force and free energy as<br>
> below from umbrella sampling and g_wham analysis,<br>
><br>
> max. force free energy<br>
> system 1 1470 42<br>
> system 2 1647 32<br>
><br>
> system 2 has higher pulling force than system 1 and the free energy<br>
> result is different from this trend.<br>
><br>
<br>
How did you obtain the maximum force, just a single SMD trajectory? If so, I<br>
wouldn't put a lot of faith in it necessarily. Umbrella sampling is a more<br>
robust method than a single pull. You can use large numbers of pulling<br>
simulations and apply Jarzynski's equation to calculate free energy, but there<br>
are distinct caveats (although I suppose there are caveats with any method).<br>
<br>
-Justin<br>
<br>
<br></blockquote><div>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. <br>
<br>vijay. <br></div></div><br></div>