[gmx-users] H bonds energy

[David L. Bostick]

Hello,

You may want to take a look at the old water model paper by Rahman and
Stillinger. There, they calculate the distribution of energies between all
water molecule pairs, and identify an energetic cutoff at a minimum in the
tail of the distribution. You then have an energetic criterion for hydrogen
bonding.  This, then would be the meaning of the energy of a H-bond. You
could in principle do this for any 2 (roughly electroneutral) groups of
atoms in order to identify a hydrogen bond.

There is no code for this in gromacs, per se.

David


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David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick
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On Tue, 8 Nov 2005, Robson Honorato wrote:

> Hi dear all,
> How can I get the H bonds energy from my simulation?
> I get the H bonds as a function time only, but I need the energy.
> Regards,
>
> Robson Honorato
> Fundamental Chemistry Department
> Federal University of Pernambuco - Brazil
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