[gmx-users] Re:how to get the the force plot after pulling

[huifang liu]

> 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>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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).
 Hi, Thomas,

Thank you very much for your reply. It is really helpful to me. But there
are two things that still confuse me.
My .pdo file is like this:
# AFM   3.0
# Component selection: 1 1 1
# nSkip 1
# Ref. Group 'USK'
# Nr. of pull groups 1
# Group 1 'UNK'  afmVec -0.179258 0.695867 -0.695439  AfmRate 0.005000  AfmK
500.000000
#####
0.000000        2.739100        6.984308        2.668408
4.016277        4.016280        2.026386        2.026388
7.623277        7.623278
0.002000        2.739100        6.984308        2.668408
4.016277        4.016278        2.026386        2.026394
7.623277        7.623271
0.004000        2.739100        6.984308        2.668408
4.016277        4.016276        2.026386        2.026401
7.623277        7.623264
0.006000        2.739100        6.984308        2.668408
4.016277        4.016275        2.026386        2.026408
7.623277        7.623257
0.008000        2.739100        6.984308        2.668408
4.016277        4.016273        2.026386        2.026415
7.623277        7.623250
0.010000        2.739100        6.984308        2.668408
4.016277        4.016271        2.026386        2.026422
7.623277        7.623243
0.012000        2.739100        6.984308        2.668408
4.016277        4.016269        2.026386        2.026429
7.623277        7.623236
0.014000        2.739100        6.984308        2.668408
4.016277        4.016267        2.026386        2.026436
7.623277        7.623229
0.016000        2.739100        6.984308        2.668408
4.016277        4.016266        2.026386        2.026443
7.623277        7.623222
0.018000        2.739100        6.984308        2.668408
4.016277        4.016264        2.026386        2.026450
7.623277        7.623215
0.020000        2.739100        6.984308        2.668408
4.016277        4.016262        2.026386        2.026457
7.623277        7.623208
0.022000        2.739100        6.984308        2.668408
4.016277        4.016260        2.026386        2.026464
7.623277        7.623201
Since the column 5, 7, 9 only changed after every picosecond and column 6,
8,10 changed per 0.002 ps (i set the dt=0.002 in .mdp file). I am wondering
whether the column 5,7,9 stand for Sx, Sy, Sz or Px, Py, Pz as you said. If
you are right, why the Px, Py, Pz keep the same every picosecond? Is this
beacuse that i set the nstxout=500 in the .mdp file (1ps=dt*nstxout).

>
> 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.

If i want to calcutate the force in the pulling direction,
F=sqrt(Fx*Fx+Fy*Fy+Fz*Fz) ?

Thank you so much.

Huifang

>
>
> Hope this helps.
> Thomas



>
> > 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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>
> --
> 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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