Hi, Rajendras,
To add a bit to what Aron said, you can go about solving this problem a
number of ways. I will touch on two.
First, you can get at the PMF using umbrella sampling, where your free
energy would be a function of the distance, for example, across the bridge.
Second, you can follow Aron's recommendations to just let the system sample
itself into equilibrium. This latter bit "can be" obtained through
straight, unbiased, standard MD at your temperature of interest. However,
you will almost certainly hit a sampling barrier - you're not getting
closer to the equilibrium distribution per day that makes sense in practice
(e.g. you would need to run for 100 days nonstop on 12 cores to get a
proper estimate of the equilibrium) To scale this barrier, you could use
REMD.
You may be familiar with US and REMD already, but if you are not, it may
take some reading to determine what path you will take...
Although there's a bounty of choice articles out there on the matter,
here's a selection from Professor Carlos Simmerling's laboratory :::
Investigation of salt bridge stability in a generalized born solvent model
Geney, R.; Layten, M.; Gomperts, R.; Hornak, V.; Simmerling, C.
Journal of Chemical Theory and Computation 2006
Evaluation of salt bridge structure and energetics in peptides using
explicit, implicit, and hybrid solvation models
Okur, A.; Wickstrom, L.; Simmerling, C.
Journal of Chemical Theory and Computation 2008
Improving the description of salt bridge strength and geometry in a
Generalized Born model
Shang, Y.; Nguyen, H.; Wickstrom, L.; Okur, A.; Simmerling, C.
J Mol Graph Model 2011
HTH,
Kevin
--
-- - -
HK
-----------------------------------------------------------------------------
Kevin Hauser
The Louis and Beatrice Laufer
Center for Physical and Quantitative Biology
at Stony Brook University
National Institutes of Health,
Chemical Biology Interface Training Program Fellow
The Department of Chemistry
Stony Brook University
Stony Brook, New York 11794
Phone: (561) 635.1848
Email: 84hauser.gmail.com
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Received on Sun Jul 22 2012 - 16:30:02 PDT
