[gmx-users] pulling force vs free energy

[Justin A. Lemkul]

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

-- 
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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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