mechanical force calculation

From: Gaurav Sharma (sharma_at_coe.neu.edu)
Date: Thu Aug 31 2006 - 22:23:55 CDT

Hi All,

I have a protein system consisting of two helical chains which move
apart during an MD run. I want to calculate the mechanical force
generated between the two chains during the conformational change. I
recently came across this paper:
Ioan Kosztin, Robijn Bruinsma, Paul O'lague, and Klaus Schulten,
``Mechanical force generation by G-proteins'',
Proceedings of the National Academy of Sciences USA 99, 3575 (2002)

in which the author used NAMD and calculates a similar force by joining
the COM of a group of atoms on the two chains by a harmonic spring with
a known spring constant and finally calculating the force as F = k(X-a),
where X is the initial separation between the two groups and 'a' is the
separation during the MD run. I would like to do a similar thing with my
system but am not sure how to define the harmonic spring for the
simulations.

My first impression is to use the tclForce functionality to implement
the spring. Is it possible to modify the smd.tcl script from the SMD
tutorial by defining two group of atoms and constraining them together
through a harmonic potential with a known spring constant?

Please let me know your thoughts about this approach. Has someone
already implemented such a script? I would grealty appreciate if you
could help me out with writing such a script as I do not have any
scripting experience.

Thanks,
Gaurav

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