Heirarchical Constrained Molecular Dynamics Simulations for Proteins

Abstract

Here we report a constrained molecular dynamics method that allows molecular models ranging from all-torsion to freezing parts of the protein as rigid body connected by flexible hinges, and studying the dynamics of proteins. This method is known as GNEIMO (Generalized Newton-Euler inverse mass operator method). We have derived new algorithms to assign initial velocities in the torsional space that obey the Boltzmann distribution. The effect of assigning initial velocities in the dihedral space (as opposed to transforming the Cartesian velocities to dihedral velocities), on the time taken for equilibrating the molecular system is analyzed.