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