Generally:
Using a higher force constant and / or pulling velocity drives the
system faster out of equilibrium, which results in higher rupture forces.
Varying the force constant has two effects. The softer the potential is,
the larger are the fluctuations in the coordinates but the lower are the
fluctuations in the force (see Paper: Biophysical Journal Volume 72
April 1997 1568-1581). So a lower force constant gives 'nicer looking'
force-extension curves.
Problem with a low force constant is that it's harder to detect
intermediates in the system (especially if they have small energy
barriers). I think the was a paper from Grubmüller which showed this in
a picture. But i don't remember the title and only believe it was from
Grubmüller. But one this effect also in the PMF obtained from
Jarzynski's equality - here a too low force constant (lower than the
curvature of the PMF) gives deviations from the exact result (G. Hummer,
A. Szabo; PNAS 107 (50): 21441-21446, 2010).
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=umbrella
pull_geometry=direction
pull_vec1=1 0 0
pull_start=yes
pull_ngroups=1
pull_group0=surf
pull_group1=poly
pull_rate1=0.01
pull_k1=1000
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
The slope and the shape of the force-extension curve (extension = v*t)
depends on the underlying potential surface. A linear increasing force
corresponds (in first approximation) to an harmonic potential. In
experiments where they use sometimes long linker molecules, one observes
a force which increases steeper with increasing extension -> this
corresponds to a Worm-Like-Chain.
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.
Andy
Greetings
Thomas
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