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

[Marc Baaden]

Hi,

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
as

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)


NB:
Calculated values are from the xtc file with 100000 precision
I did write out every timestep.


  Marc Baaden

-- 
 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
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