[gmx-users] the sign of the bonding energy term

[Erik Lindahl]

On Friday, Mar 7, 2003, at 04:12 US/Pacific, Yong Kong wrote:

> Dear GROMACS team/users!
>
> I am a new uesr, and have a general question on  the bonding 
> interactions in
> GROMACS (bonds, angle and dihedral). It seems that GROMACS treats all 
> the three
> types of bonding as positive terms. That means for a non-protein 
> system with
> zero partial charge on atoms the calculated potential energy must be 
> positive,
> is my understanding right? And if that's true, the energy minimization 
> still
> works? Should I change the signs of the bonding parameters manually to 
> maintain
> the total/potential energy negative?
>

I don't know of any forcefield that uses negative energies for bonded 
interactions; if you were to change the sign, the most unfavorable 
state of a bond would be its equilibrium value and the best state when 
the two atoms are at a distance of infinity. That will obviously crash 
any simulation.

Don't change any parameters whatsoever; the sign of the energy doesn't 
have anything to do with the minimization :-)

Cheers,

Erik