Symplectic integration of closed chain rigid body dynamics with internal coordinate equations of motion

Internal coordinate molecular dynamics (ICMD) is a recent efficient method for modeling polymer molecules which treats them as chains of rigid bodies rather than ensembles of point particles as in Cartesian MD. Unfortunately, it is readily applicable only to linear or tree topologies without closed flexible loops. Important examples violating this condition are sugar rings of nucleic acids, proline residues in proteins, and also disulfide bridges . This paper presents the first complete numerical solution of the chain cl osure problem within the context of ICMD. The method combines natural impli cit fixation of bond lengths and bond angles by the choice of internal coor dinates with explicit constraints similar to Cartesian dynamics used to mai ntain the chain closure. It is affordable for large molecules and makes pos sible 3-5 times faster dynamics simulations of molecular systems with flexi ble rings, including important biological objects like nucleic acids and di sulfide-bonded proteins. (C) 1999 American Institute of Physics. [S0021-960 6(99)50928-8].