[gmx-users] pulling force vs free energy

[Vijayaraj]

>
> Message: 4
> Date: Wed, 16 Nov 2011 09:34:02 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] pulling force vs free energy
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4EC3C9DA.7040400 at vt.edu>
> 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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