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

[Yong Kong]

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?

Thanks

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Kong, Dr. Yong
Max-Planck-Institute for Metals Research
Dept. Theory of Mesoscopic Phenomena
Heisenbergstr. 3
D-70569 Stuttgart

Phone: ++49(0)711/689-3566
Fax  : ++49(0)711/689-3512

E-mail  : Y.Kong at mf.mpg.de
Internet: http://shasta.mpi-stuttgart.mpg.de/
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