Molecular Dynamics - Small Molecule

Objective

To determine and optimize a protocol for molecular dynamics simulation to calculate radial distribution function.

  • Parametrization and input file preparation is done with 'ANTECHAMBER', 'PARMCHK' and 'LEAP'
  • Two methods used to restrain internal coordinates 'IBELLY' (Ibelly artificially sets to zero the forces on all of the atoms in the fixed portion at the end of each energy/force evaluation.) and 'NTR' with suitable force constants.
  • To determine the optimized protocol, systematic modifications in the minimization and molecular dynamics parameters like restraints, termostat, time-step were done.

Inference: