**From:** Jason Swails (*jason.swails_at_gmail.com*)

**Date:** Tue Mar 04 2014 - 20:04:38 CST

**Next message:**Shyno Mathew: "Restarting an FEP simulation"**Previous message:**Kenno Vanommeslaeghe: "Re: VDW energy: positive or negative?"**In reply to:**PANAGIOTA KYRIAKOU: "Re: VDW energy: positive or negative?"**Next in thread:**Kenno Vanommeslaeghe: "Re: VDW energy: positive or negative?"**Reply:**Kenno Vanommeslaeghe: "Re: VDW energy: positive or negative?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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

**Next message:**Shyno Mathew: "Restarting an FEP simulation"**Previous message:**Kenno Vanommeslaeghe: "Re: VDW energy: positive or negative?"**In reply to:**PANAGIOTA KYRIAKOU: "Re: VDW energy: positive or negative?"**Next in thread:**Kenno Vanommeslaeghe: "Re: VDW energy: positive or negative?"**Reply:**Kenno Vanommeslaeghe: "Re: VDW energy: positive or negative?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Thu Dec 31 2015 - 23:20:34 CST
*