[gmx-users] HBonds between molecules

Justin A. Lemkul jalemkul at vt.edu
Sun Mar 18 14:43:33 CET 2012

Hovakim Grabski wrote:
> Dear Gromacs users,
> I ran a simulation with 13 Hypericin molecules in water for 10 ns and 7 
> of them formed an aggregate.Is there any way to find out between what 
> molecules and atoms Hbonds were formed?

Yes, see the various options that g_hbond provides, particularly -hbn and -hbm.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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