Hi all,
I am now trying to do simulations with ions parameters from Chen et al (J.
Phys. Chem. B 2007, 111, 11884-11887) and ffamber99sb together. After
generate the prmtop file, I need to identify the Lennard-Jones parameters
for NaCl and change them accordingly. I have read the prmtop format and
identify the IAC, ICO for NaCl, then I found CN1 and CN2 for NaNa, NaCl,
ClCl parameters. But I am confused how the CN1 and CN2 are calculated. The
following is what I used:
Lennard-Jones interaction:
A/(r^12)-B/(r^6)
where A is LENNARD_JONES_ACOEF in prmtop file, and B is LENNARD_JONES_BCOEF
in prmtop file.
Then (A/B)^(1/6) should give sigma(NaCl), and
sigma(NaCl)=(R(Na)+R(Cl))/(2^(1/6)).
Sigma(NaCl) I got from A,B of prmtop and from R(Na), R(Cl) of parm doesn't
agree with each other. I am really confused how CN1 and CN2 are calculated.
Could you please give me a hint if you know how these parameters are
calculated? Thanks a lot.
Jianhui
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Received on Sun Jan 17 2010 - 09:30:02 PST
