Molecular dynamics simulation energy conservation

Kitchen, D.B., Hirata, F., Westbrook, J.D., Levy, R. Conserving energy during molecular dynamics simulations of water, proteins, and proteins in water. J. Comput. Chem. 11 (1990) 1169-1180. 

Teleman, O. An efficient way to conserve the total energy in molecular dynamics simulations boundary effects on energy conservation and dynamic properties. Mol. Simul. 1 (1988) 345-355. 

Successful first-principles molecular dynamics simulations in the Car-Paxrinello framework requires low temperature for the annealed electronic parameters while maintaining approximate energy conservation of the nuclear motion, all without resorting to unduly small time steps. The most desirable situation is a finite gap between the frequency spectrum of the nuclear coordinates, as measured, say, by the velocity-velocity autocorrelation function. 

Since its inception, r-RESPA has proven to be indispensable for molecular dynamics simulations of large systems. Using r-RESPA to break down the force calculations into different time scales has given rise to the ability to take significantly larger fundamental time steps without suffering a decrease in the energy conservation of the simulation. 

Smooth Cut-Off. In molecular dynamics simulations it is convenient to have a pair potential with compact support for efficiency reasons. While it is possible to simply use a split function (setting the potential—or force—to zero outside some finite range), this has undesirable consequences for energy conservation if the function is not sufficiently smooth. Consider the alternative [346] ... 

The ENCAD (energy calculations and dynamics) force field has been developed by Levitt et al. for the molecular dynamics simulations of proteins and nucleic acids in solution. It employs all-atom force field parameters. For condensed phase simulations the new three-center, flexible water model has been developed. The stress has been laid on the energy conservation effect during molecular dynamics simulations without coupling simulated systems to the thermal bath. The following expression has been used to calculate potential energy of the molecular systems ... 

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