[gmx-users] g_hbond on trajectory

[Justin Lemkul]

On 6/2/15 5:01 AM, Jennifer Vo wrote:
> Dear All,
> I used g_hbond to analyze the possible hydrogen bonds between protein and
> solvent (water) over the trajectory with this command:
> g_hbond -s md-1.tpr -f md.xtc -n index.ndx -hbm hbmap.xpm -num hbnum.xvg -g
> hbond.log -dist hbdist.xvg -nhbdist nhbdist.xvg
>
> The log file showed me:
> ....
>    SER141OG      SER141HG     SOL2920OW
>    SER141OG      SER141HG     SOL4449OW
>    SER141OG      SER141HG     SOL5073OW
>    SER141OG      SER141HG     SOL11886OW
>    SER141OG      SER141HG     SOL13715OW
> ....
> I wonder if this calculation is based on one coordinate file (if yes, which
> one!?) or the average structure over trajectory?

Trajectory analysis is done for every frame in the trajectory.  The log output 
just indicates that different waters were hydrogen bonded to that particular Ser 
at different times.

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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