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 hydrogen bonds number in trajectory by Gromacs...... With Best Wishes, Rama David
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
