[gmx-users] AFM pulling: after bond-breakage force does not drop to zero

Thomas Schlesier schlesi at uni-mainz.de
Mon Aug 11 16:24:45 CEST 2008

Dear all,
I simulate pulling experiment with the AFM-option in GROMACS. I
calculate the forces from the .pdo file:
F = k_c (/spr/ - /pullg/)
with F the force, k_c the springconstant. spring is the position of the
spring and /pullg/ the position of the pullgroup. after the
bond-breakage the forces have a much lower value, but they do not drop
to zero.
in this picture is one of my force-distance-curves:


My problem is I do not understand why (after the bond-breakage) the mean
value of the force is not zero. The simulations are made in vacuum, so
there is no friction.
When I use a lower the springconstant the distance (/spr/ - /pullg/)
gets greater. Greater springconstant yields a lower distance.

Has anybody of you an idea why the mean value of the forces does not
drop to zero, or have seen anything similar?
Thanks for an answer.

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