Molecular dynamics simulation method and apparatus

A computer-assisted method for generating a dynamic model of a molecule, said molecule including a predetermined set of atoms in a predetermined atomic structure, comprising the steps of:

• A. generating model data for said molecule, said model data defining
• i. bodies corresponding to groups of one or more of said atoms of said molecule, and
• ii. flexure elements, each of said flexure elements defining an interconnection of two of said bodies, said interconnection having predetermined degrees of freedom,
• B. generating first base data representative of position coordinates and velocities of the atoms of said molecule measured with respect to a reference coordinate system,
• C. processing said first base data and said model data including the substeps of:
• i. for each of said bodies:
• a. identifying a body coordinate system for said body,
• b. determining for each atom in said body the position, velocity and acceleration measured with respect to said body coordinate system,
• ii. defining hinge constraints between adjacent ones of said bodies, said hinge constraints being defined with respect to said body coordinate systems of said adjacent ones of said bodies, and said hinge constraints defining a component of a vector {.beta.} representative of generalized coordinates of all of said bodies,
• iii. determining from said generalized coordinates, hinge rates corresponding to ##EQU36## and hinge accelerations corresponding to ##EQU37## iv. determining an equation of motion for each of said bodies, said equations of motion defining a vector {U.sub.i }, where i is an index representative of said bodies, and
• v. recursively determining from [U.sub.i ] the absolute position and velocity of each of said bodies.

A computer system for generating a dynamic model of a molecule, said molecule including a predetermined set of atoms in a predetermined atomic structure, comprising:

• A. means for providing information representative of said atomic structure, and
• B. model data means for generating model data for said molecule, said model data defining
• i. rigid bodies corresponding to groups of one or more of said atoms of said molecule characterized by substantially no relative movement therebetween,
• ii. flexible bodies corresponding to groups of two or more atoms of said molecule characterized by relative movement therebetween, and
• iii. flexure elements, each of said flexure elements defining an interconnection of two of said rigid bodies and said flexible bodies, said interconnection having predetermined degrees of freedom.

A new computer system for generating a dynamic model of a molecule, said molecule including a predetermined set of atoms in a predetermined atomic structure, comprising:

• A. means for providing information representative of said atomic structure, and
• B. model data means for generating model data for said molecule, said model data defining
• i. bodies corresponding to groups of one or more of said atoms of said molecule, and
• ii. flexure elements, each of said flexure elements defining an interconnection of two of said bodies, said interconnection having predetermined degrees of freedom,
• B. first base data means for generating first base data representative of position coordinates and velocities of the atoms of said molecule measured with respect to a reference coordinate system,
• C. processor means for processing said first base data and said model data including the substeps of:
• i. for each of said bodies:
• a. identifying a body coordinate system for said body,
• b. determining for each atom in said body the position, velocity and acceleration measured with respect to said body coordinate system,
• ii. defining hinge constraints between adjacent ones of said bodies, said hinge constraints being defined with respect to said body coordinate systems of said adjacent ones of said bodies, said hinge constraints defining a component of a vector {.beta.} representative of generalized coordinates of all of said bodies,
• iii. determining from said generalized coordinates, hinge rates corresponding to ##EQU40## and hinge accelerations corresponding to ##EQU41## iv. determining an equation of motion for each of said bodies, said equation of motion defining a vector {U.sub.i }, where i is an index representative of said bodies, and
• v. recursively determining from {U.sub.i } the absolute position and velocity of each of said bodies.