I want number of hydrogen bond between two groups using the commands below:
gmx_mpi make_ndx -f npt_prod1.gro -o index2.ndx
gmx_mpi hbond -f npt_prod1.xtc -s npt_prod1.tpr -n index2.ndx -num emim-cyno.xvg
when I checked my trajectories in vmd I can see hydrogen bond between these particular groups (at 3.5 A and 30 degree geometric criteria) however when I choose those particular group in gromacs it was shown that ,no donors and accept-or found.Can anyone have suggestions?why I am not getting hbonds between these groups.
The message you got from gmx hhond say that it does not find any donor or acceptor, that mean that gmx hbond does not recognize the atoms of the two groups neither as donor nor as acceptor. And that is the reason why it does not find the H-bond).
gmx hbond recognizes OH and NH groups as donors, O is an acceptor always, N is an acceptor by default, but this can be switched using -nitacc.
and the two groups for analysis must be either identical or non-overlapping.
Are those conditions you are working with? Are you using a standard implementation of an atomistic force field ?