Digitally filtered molecular dynamics: The frequency specific control of molecular dynamics simulations

A new method for modifying the course of a molecular dynamics computer simu lation is presented. Digitally filtered molecular dynamics (DFMD) applies t he well-established theory of digital filters to molecular dynamics simulat ions, enabling atomic motion to be enhanced or suppressed in a selective ma nner solely on the basis of frequency. The basic theory of digital filters and its application to molecular dynamics simulations is presented, togethe r with the application of DFMD to the simple systems of single molecules of water and butane. The extension of the basic theory to the condensed phase is then described followed by its application to liquid phase butane and t he Syrian hamster prion protein. The high degree of selectivity and control offered by DFMD, and its ability to enhance the rate of conformational cha nge in butane and in the prion protein, is demonstrated. (C) 2000 American Institute of Physics. [S0021-9606(00)52805-0].