[gmx-users] About hydrogen bond ..

rama david ramadavidgroup at gmail.com
Mon Apr 23 16:20:27 CEST 2012

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 ???

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

With Best Wishes,
Rama David
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