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.