On 7/9/13 12:56 PM, rookie417 wrote:
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
Note that what you're doing is not umbrella sampling, but steered MD, which is a
nonequilibrium process. The "umbrella" pulling method is unfortunately named,
as it is just a harmonic potential. Umbrella sampling is a separate procedure,
one that uses the "umbrella" method and zero pull rate.
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
Basically, yes. No one (to my knowledge) has done a systematic study of such
parameters. I suspect that is because they are largely dependent upon the
system and the interactions you are trying to disrupt.
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.
There will be an initial increase in force until restoring forces are overcome,
at which point forces decrease and level off. I don't know about a comparison
of force constants, but I suspect the result should be similar to varying the
pull rate. The progression will be steeper with faster pulling or a harder
force constant, more shallow with slow pulling or a soft constant. We addressed
this topic in the supporting information for
http://pubs.acs.org/doi/abs/10.1021/jp9110794.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Associate
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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