[gmx-users] How to calculate PMF after AFM pulling

[Justin A. Lemkul]

huifang liu wrote:
> 
> Hi Justin,
>  
> Thank you for your reply, but i am still a little confused. You said in 
> principal I should be able to extract a potential of mean force from an
> AFM run by simply integrating the average force along the reaction 
> coordinate and if I have the average force as a function of position, I
> could simply integrate that to get the PMF. However, actually, i don't 

I didn't say that.  The post I pointed you to did :)

> know how i can get the average force as a function of position and apply 
> them in the PMF calculation. Could you give me some suggestion?
>  

Your .pdo file should have the forces, if I remember the old (3.3.x, right?) 
file format correctly.  Then something like g_traj can extract coordinates from 
your trajectory.  Also a good reference (and there is a ton of stuff in the list 
archive about this, hint):

http://www.gromacs.org/pipermail/gmx-users/2002-August/002241.html

I've not tried to do PMF analysis this way.  It is much easier under 4.0 now to 
use umbrella sampling since g_wham now works.  It was non-functional (or buggy 
at best) in previous versions.

-Justin

> Thanks a lot.
>  
> Huifang
> -- 
> Huifang Liu (Ph.D. Student)
> School of Pharmacy
> Fudan University
> 
> 138 Yi Xue Yuan Rd.          Tel: (86-21)54237419 (O)
> Shanghai, China, 200032     Cell phone: +86-13764669357
> E-mail: huifangliu1985 at gmail.com <mailto:huifangliu1985 at gmail.com> Fax: 
> (86-21)54237264
> 
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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