Structured Water molecules on the Protein Surface

Objective

To determine the range of structured water molecules on the protein surface.

  • Molecular dynamics simulation of myoglobin molecule was carried out in explicit water using NAMD.
  • After initial minimization and 20ps equilibration, MD snapshots were collected at 1ps interval for 100ps.
  • Perl codes are written to run Hbplus program to calculate hydrogen bonds between water and protein molecule in each snapshot.

Inference: