From: Shayon Bhattacharya (shayon.bhattacharya_at_gmail.com)
Date: Tue Sep 29 2015 - 10:20:36 CDT
Dear NAMD list,
I am running simulations with various TIP4P water models (TIP4P, TIP4P-Ew,
TIP4P/2005, etc) for my protein to test a certain feature and choose the
right model for my simulation - all using CHARMM36 FF for proteins. I have
used the tip4p kit from Peter -
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2011-2012/0322.html
with the pre-equilibrated water box, and also using this for the other
water models (generating psfs of boxes with different topologies).
I see that the Mackerell website have these tip4p water model parameters
(in toppar stream files) with no values (they are zeroes) on the Hydrogen
Lennard-Jonnes parameters - epsilon and Rmin/2 as used in charmm
convention, whereas the parameter file from Peter has a Rmin/2 value of
0.0250, while the epsilon is 0. Same applies for tip4p/2005, where the
parameter file from Jordi Faraudo has hydrogen LJ values of -0.046 and
0.2245 respectively for epsilon and Rmin/2, whereas the one from Mackerell
website had zeroes in place.
Knowing that the oxygen LJ parameters are what matters, and the vdw radii
for oxygen is bigger than hydrogen, my question is do the LJ parameters for
hydrogen really matter? If so, why such discrepancies in values for NAMD
compatible Charmm conventions?
thank you,
Shayon
-- Shayon Bhattacharya PhD student Department of Physics and Energy University of Limerick, Ireland
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