[gmx-users] how to get the the force plot after pulling, dynamic simulation using GMX-3.3

Thomas Schlesier schlesi at uni-mainz.de
Thu Mar 19 14:12:03 CET 2009

> Date: Thu, 19 Mar 2009 13:52:09 +0800
> From: huifang liu <huifangliu1985 at gmail.com>
> Subject: [gmx-users] how to get the the force plot after pulling
>         dynamic simulation using GMX-3.3
> To: gmx-users at gromacs.org
> Message-ID:
>         <e523c6be0903182252i114666bam4bbe591a10a30677 at mail.gmail.com>
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> I am recently doing a SMD. I think i did it very well. But i don't know how
> to get the force plot. Is there some one can give me a suggestion?
> Thank you very much.
At the end of the SMD you should have obtained a .pdo file. In that file
the time and the coordinates of the reference- (R), pull-group (P) and
of the spring (S) are written. If i remember correctly it was: t, Rx,
Ry, Rz, Px, Sx, Py, Sy, Pz, Sz. If you have more pullgroups then you
have first the x-coordinates of P and S, then y-coordinates ... (look in
the manual or the header of the .pdo; or for t=0 you should know the
position of all particals and springs and can calculate a little bit to
see which entry corresponds  to which group).
For the force-calculation: The force is the deflection of the spring
times  the force-constant of the spring ->  Fx =  k(Sx-Px) ... for the
other directions it's analog. Then you can calculate the magnitude of F
and plot it against the time (if you are only interested in the
magnitude of force). Or you can calculate the force in the pulling
direction and plot it against time.

Hope this helps.
> 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 Fax: (86-21)54237264
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