[gmx-users] AFM pulling - how to get force-extension curves

Peter Tieleman tieleman at ucalgary.ca
Wed Jan 23 15:52:54 CET 2002


As reference position it takes the position at t=0 of the group you're 
pulling. The way it's done in the distribution, it doesn't do (v*T) but 
instead adds the displacement every step. This is not a great idea and 
I've changed it in some local code that should show up in cvs sometime. 
Try running in double precision and see if your output makes more sense. 
I don't remember for sure but if you use verbose in the pulll parameter 
file it might tell you the position of the string too.


Marc Baaden wrote:

>I am trying to do some AFM pulling with Gromacs.
>Basically I think I got it to work correctly, but
>I am not able to reproduce the Gromacs output in
>pull.pdo (forces).
>I assumed that the forces in the output are calculated
>F = k * (v*T - extension)
>[or maybe .. (extension - v*T)]
>where F is the force in kJ/mol
>k the force constant in kJ/(mol*nm)    [I used 100]
>T is the step (0,1,...)
>v is the pull rate in nm/timestep      [I used 0.00005]
>extension is the distance between fixed reference group and
>moving atom in nm
>v*T corresponds to the cantilever position, but what is its
>initial value ?
>As extension I used the distance in z calculated from the xtc-trajectory
>using g_dist and the same 2 index groups given for the AFM pulling.
>With these values I tried to recalculate the forces, but they are not the
>same ! (assuming a fixed constant offset for v*T as origin)
>Any idea what I am doing wrong ?
>Basically I want to be sure that I calculate the right extension
>(the one which is corresponding to the applied force)
>Or is there another (easier and foolproof) way to get the force-extension
>curve ? (as Gromacs only writes out the forces but not the extension)
>Calculated values are from the xtc file with 100000 precision
>I did write out every timestep.
>  Marc Baaden

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