Thomas C. Bishop, Helmut Heller, and Klaus Schulten.
Molecular dynamics on parallel computers: Applications for
theoretical biophysics.
In Rajiv K. Kalia and Priya Vashishta, editors, Toward Teraflop
Computing and New Grand Challenge Applications, pp. 129-138. Nova Science
Publishers, Inc., New York, 1995.
BISH95A
Molecular dynamics is a valuable aid for refining the observed structure of biopolymers, for understanding the structure-function relationship of biopolymers, and for the rational design of drugs. In order to accurately characterize biopolymers, it is often necessary to explicitly include solvent or other environments, namely water, ions or cellular membranes resulting in system sizes of tens of thousands of atoms. The resulting large systems can only be simulated on massively parallel computers. A molecular dynamics program, EGO, has been developed to run on parallel computers in order to simulated large systems. EGO, which was written in OCCAM II and runs on transputers, has been used to conduct simulations of biologically significant systems. Two transputer systems, based on the INMOS T805 processor, have been employed for molecular dynamics: a custom built 60-node system and Parsytec GCel-64 with 64-nodes. EGO has recently been rewritten in C to run under the machine-independent coordination languages Charm and PVM, so that simulations can be conducted on a workstation cluster. The program EGO has been applied to simulations of a protein-DNA complex in a water envelope resulting in a system of 13,500 atoms. The simulations have required dedicated computational resources of one month per simulation. Results from the simulations indicate that the so-called DNA binding domain of the glucocorticoid receptor protein induces a bend of approximately 35 degrees in the DNA.
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