[gmx-users] How to calculate PMF after AFM pulling
Justin A. Lemkul
jalemkul at vt.edu
Fri Mar 27 11:47:51 CET 2009
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):
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.
> Thanks a lot.
> 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:
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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