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: huifangliu1...@gmail.com <mailto:huifangliu1...@gmail.com> Fax:
(86-21)54237264
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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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