[gmx-users] Umbrella sampling and dividing the forces into mean force + friction force + random force
gozdeeergin at gmail.com
Wed Nov 25 14:02:54 CET 2015
Dear gromacs users,
I would like ask a question about the force of umbrella sampling.
I did umbrella sampling by pulling a water molecule from gas phase to
organic coated bulk water.
I estimated the free energy profile on this reaction coordinate.
In order to calculate the random force-force auto-correlation I need to
extract the random force on pulled molecule. The force along a reaction
coordinate consists of three terms, (i) the mean force as the derivative of
the free energy surface, (ii) friction, and (iii) random force.
I used gromacs tool g_traj to extract the force on pulled molecule however
I do not know how to get the random (iii) force out of it.
I would greatly appreciate it if you kindly give me an advise about a way
to extract random forces from the overall forces?
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