scaling non-bonded interactiion parameter for specific pairs

Date: Fri Feb 27 2015 - 13:15:11 CST

Dear NAMD user,

I am simulating a protein system in presence of TMAO molecule in which I
used the most updated charmm general force field for TMAO. Most of
simulation studied of TMAO have employed Kast model. Garcia et al showed
that this TMAO model, Kast model, does not provide acceptable osmotic
pressure compare to experimental results ( Molecular Mechanism for the
Preferential Exclusion of TMAO from Protein Surfaces, J. Phys. Chem. B, 2012
, 116 (40), pp 12095–12104). They improved this model by decreasing Lj
potential well only for TMAO-TMAO interactions which make them less
favorable to each other and TMAO-water remained the same. To applying their
model into my system and compare it with charmm results, I was wondering if
there is a way to scale Lj parameter only for specific pairs, for instance
all TMAO-TMAO, in NAMD?!


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