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


Phillips, S. C., Essex, J. W. and Edge, C. M. (2000) Digitally filtered molecular dynamics: The frequency specific control of molecular dynamics simulations. Journal of Chemical Physics, 112, (6), 2586-2597. (doi:10.1063/1.480832).

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Description/Abstract

A new method for modifying the course of a molecular dynamics computer simulation is presented. Digitally filtered molecular dynamics (DFMD) applies the well-established theory of digital filters to molecular dynamics simulations, enabling atomic motion to be enhanced or suppressed in a selective manner solely on the basis of frequency. The basic theory of digital filters and its application to molecular dynamics simulations is presented, together 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 the Syrian hamster prion protein. The high degree of selectivity and control offered by DFMD, and its ability to enhance the rate of conformational change in butane and in the prion protein, is demonstrated.

Item Type: Article
Related URLs:
Keywords: potential functions, nucleic-acids, force-field, proteins, trajectories, echoes, motions, water
Subjects: Q Science
Q Science > QD Chemistry
Divisions: University Structure - Pre August 2011 > School of Chemistry
ePrint ID: 19039
Date Deposited: 21 Dec 2005
Last Modified: 27 Mar 2014 18:08
URI: http://eprints.soton.ac.uk/id/eprint/19039

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