[gmx-users] Umbrella sampling- force vs time plots

rookie417 lsurampu at tulane.edu
Tue Jul 9 18:56:35 CEST 2013

Hello all,

I am trying to understand the force vs time plots using Gromacs' umbrella
sampling method. I am trying to pull a short polymer chain from the interior
of a micelle and see what the PMF looks like. I use the following parameters
to run the pulling simulation for 500ps to pull the polymer over a distance
of 5nm:

pull_vec1=1 0 0

After the simulation, pullf.xvg plot I obtained is a linearly increasing
plot with time and similar result when pull_rate1=0.001 nm per ps. I am not
sure if this is right. My question is, on what basis do we select the
optimum pull_rate1 and pull_k1 for a particular system? Or is it just a
choice of parameters as long as the system does not deform? How does an
ideal force-time plot look like and does the choice of pull_k1 affect the
histogram?  It appears, the entire procedure depends on the choice of input
of these two variables. I would greatly appreciate if someone can explain
this concept.

Thanks a lot.

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