[gmx-users] h_bond

[Shahid Nayeem]

Dear all

I want to get number of hydrogen bonds between solvent(water) and alpha
helix or beta sheet along the trajectory. Secondary structure of protein
changes along the trajectory. Is it possible for gromacs to first find the
secondary structure of snapshot and then calculate hydrogen bonds between
SOL and each of the the secondary structure and then same for the next
snapshots.

shahid