[gmx-users] RMSD of a single water molecule.

[Seketoulie Keretsu]

Dear User,

I am trying to find the RMSD of a single water molecule which showed H-bond
interaction with a ligand in a protein-ligand system simulation. The study
was to explore the role of water in the binding of the ligand at the
receptor. The RMSD of the water molecule (using the protein backbone for
fitting) huge variation between 2 to 10 angstrom. VMD visualization showed
that the water molecule was basically all over the simulation box and not
at the vicinity of the ligand. Is it right to say from this observations
that:
1. The H-bonds interaction of ligands with water molecule are transient ?
2. Water molecules are indeed all over the simulation box ?
3. gmx hbond analysis, gmx distance analysis led me to believe that there
are interaction with water through out the simulation; just not the same
water molecule . Would that be right ?

Will appreciate if you can advise.
Thank you.

Sincerely,
Seke