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

huifang liu huifangliu1985 at gmail.com
Fri Mar 27 02:44:09 CET 2009

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 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?

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 Fax: (86-21)54237264
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