> > Message: 4 > Date: Wed, 16 Nov 2011 09:34:02 -0500 > From: "Justin A. Lemkul" <[email protected]> > Subject: Re: [gmx-users] pulling force vs free energy > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > 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.
vijay.
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