[gmx-users] Re: Force vs distance plot in pulling simulation?
Gmx QA
gmxquestions at gmail.com
Tue Nov 20 22:52:36 CET 2012
Hi Thomas
Thanks, that's a good point that I would have overlooked otherwise.
But is that still going to be true if one makes the PMF using wham, and
then takes the derivative of the PMF? It seems natural that if integrating
the mean force along the reaction coordinate yields the PMF (using TI, as
you outlined below), then the derivative of the PMF should give back the
mean force?
Thanks
/PK
But be aware that the force depends on the pulling velocity. If you perform
the simulation with two different pulling velocities you'll get two
different forces for each distance.
The easiest way to get the force as a function of the distance (without the
bias of the pulling velocity) would be thermodynamik intergration. This is
similar to the umbrella sampling. You set up some windows with different
distances. But instead of restraining the distance with an umbrella
potential (as in umbrella sampling) you use a constraint to fix the
distance and than can determine the constraint force.
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