[gmx-users] Water mediated hydrogen bonding

Justin Lemkul jalemkul at vt.edu
Thu Jan 15 15:11:49 CET 2015

On 1/15/15 9:03 AM, suhani nagpal wrote:
> Oh! Yes yes. Thanks for the same.
> After command -f  -s   -n  -hbm -hbn -num -dist :
> Select a group: 19
> Selected 19: 'SOL_&_OW'

Note that this will cause you to only get hydrogen bonds for which water is an 
acceptor; to get all hydrogen bonds, just use the default "SOL" group.

> Select a group: 18
> Selected 18: 'r_38-57'
> Checking for overlap in atoms between SOL_&_OW and r_38-57
> Calculating contacts between SOL_&_OW (9468 atoms) and r_38-57 (268 atoms)
> Found 268 donors and 9468 acceptors
> Making hbmap structure...done.
> Reading frame       0 time    0.000
> Will do grid-seach on 11x11x8 grid, rcut=0.55
> Frame loop parallelized with OpenMP using 16 threads.
> is this seems alright? because it has not started to read frames.

It should start right away...

> Also, are there important identifiers to be used in the command?

For simply counting hydrogen bonds, there's really nothing special to do, as 
long as the default criteria are reasonable in your judgment (they usually are).

> I meant there is 'Here' hyperlink' on this page (
> http://www.gromacs.org/Documentation/Gromacs_Utilities/g_hbond). It shows
> not found.

I fixed the link.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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