[gmx-users] H bonds energy
David L. Bostick
dbostick at physics.unc.edu
Wed Nov 9 20:07:28 CET 2005
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
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
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
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
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
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list