System and method for molecular dynamic simulation

A method for molecular dynamic simulation, comprising:

• storing data pertaining to at least one biomolecular system and instructions for performing at least one algorithm having an electrostatic interaction calculating function using a P3ME algorithm, and a multiple time step function, and subdividing forces on a basis of distances over which said forces act;
• and
• processing said data by executing said instructions in order to propagate said at least one biomolecular system from a first set of coordinates to a second set of coordinates,
• wherein said processing comprises combining k-space electrostatic interactions calculated using said P3ME algorithm with said multiple time step algorithm using a mechanism which removes a short range portion from said calculated k-space electrostatic interactions and updates said portion along with other short-range forces in said multiple time step algorithm.

A method for molecular dynamic simulation, comprising:

• separating bonded interactions from non-bonded interactions using a multiple time step algorithm;
• separating said non-bonded interactions into short-range, midrange, and long-range interactions using said multiple time step algorithm;
• using a P3ME algorithm to calculate k-space electrostatic interactions;
• and
• combining said calculated k-space electrostatic interactions with said multiple time step algorithm using a mechanism which removes the short range portion from said calculated k-space electrostatic interactions and updates said portion along with other short-range forces in said multiple time step algorithm, to propagate a protein system.

A system for molecular dynamic simulation, comprising:

• a module for separating bonded interactions from non-bonded interactions using a multiple time step algorithm;
• a module for separating said non-bonded interactions into short-range, midrange, and long-range interactions using said multiple time step algorithm;
• a module for using a P3ME algorithm to calculate k-space electrostatic interactions;
• and
• a module for combining said calculated k-space electrostatic interactions with said multiple time step algorithm using a mechanism which removes the short range portion from said calculated k-space electrostatic interactions and updates said portion along with other short-range forces in said multiple time step algorithm, to propagate the protein system.

A programmable storage medium tangibly embodying a program of machine-readable instructions executable by a digital processing apparatus to perform a method for molecular dynamic simulation, said method comprising:

• storing data pertaining to at least one biomolecular system and instructions for performing at least one algorithm having an electrostatic interaction calculating function using a P3ME algorithm, and a multiple time step function;
• and
• processing said data by executing said instructions in order to propagate said at least one biomolecular system from a first set of coordinates to a second set of coordinates,
• wherein said processing comprises combining k-space electrostatic interactions calculated using said P3ME algorithm with said multiple time step algorithm using a mechanism which removes the short range portion from said calculated k-space electrostatic interactions and updates said portion along with other short-range forces in said multiple time step algorithm.

A programmable storage medium tangibly embodying a program of machine-readable instructions executable by a digital processing apparatus to perform a method for molecular dynamic simulation, said method comprising:

• separating bonded interactions from non-bonded interactions using a multiple time step algorithm;
• separating said non-bonded interactions into short-range, midrange, and long-range interactions using said multiple time step algorithm;
• using a P3ME algorithm to calculate magnitudes of k-space electrostatic interactions;
• and
• combining said calculated k-space electrostatic interactions with said multiple time step algorithm using a mechanism which removes the short range portion from said calculated k-space electrostatic interactions and updates said portion along with other short-range forces in said multiple time step algorithm, to propagate a protein system.