[gmx-users] About hydrogen bond ..
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
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
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,
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