[gmx-users] About hydrogen bond ..

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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