[gmx-users] About hydrogen bond ..

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 23 18:43:20 CEST 2012

On 4/23/12 10:20 AM, rama david wrote:
> Hi Gromacs Friends,
>    Sorry me for asking stupid question....
> I am using gromacs 4.5.4
>    To calculate Hydrogen bonds,
>     I use the command
>     g_hbond -f nojump_fit.xtc -s input_md.tpr
>     -num hbnum_nojump.xvg -dist hbdist.xvg -ang hbang.xvg -hbm bmap.xpm
>     -n my_index.ndx
> I got the plot that show hydrogen bond .
>   When I extract the particular time pdb
> with trjconv -dump option , and visualize in pymol I can see the hydrogen bonds
> in all extracted frames..
> but when I am using the VMD for visualization with following set up for hydrogen
> bond,
> Distance cutoff - 3.5 and angle cutoff 30, (As per the manual of Gromacs) I can
> see the hydrogen bond in some frame only,
> and some frames does not show hydrogen bonds at all , though the
> hbnum_nojump.xvg shows that
> these frame has hydrogen bonds.
> Can any one tell me these reason and what to do in such conditions ???

Well, if Gromacs can see the hydrogen bonds, and PyMol can see the hydrogen 
bonds, but VMD can't - that sounds like a VMD problem.

> If you have spare time , Please help me to know the best way to determine hydrogen
> bonds number in trajectory by Gromacs......

Your g_hbond command is the correct approach.



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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