From: Jason Swails (jason.swails_at_gmail.com)
Date: Tue Mar 04 2014 - 20:04:38 CST
On Tue, Mar 4, 2014 at 7:24 PM, PANAGIOTA KYRIAKOU <kyria008_at_gmail.com>wrote:
>
> However when I checked the parameter files I use ( CHARMM 36), the epsilon
> values are negative, so the statement above is not true.
>
The previous posts have given you useful information, I'll just point out
the error in this statement. The sign of the epsilon parameters here is
entirely irrelevant (for instance, in the Amber force fields the epsilons
for each atom types are positive). The absolute value of the epsilon
parameter is the depth of the attractive well (but don't forget the LJ
potential has a repulsive 1/r^12 term that dominates at very low distances
and an attractive 1/r^6 term that attracts at longer distances).
The epsilons from each atom type are combined to give a pairwise
interaction. The canonical combining rules (Lorentz-Berthelot are used by
CHARMM, I believe) state that the combined epsilon parameters between two
atom types is defined as sqrt(epsilon_i * epsilon_j). So as you can see,
you get exactly the same combined LJ parameters whether all epsilons are
positive or negative. The choice of positive values vs. negative values is
just pedagogical.
HTH,
Jason
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