Gouthaman S. Balaraman

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Internal coordinate molecular dynamics (ICMD) methods provide a more natural description of a protein by using bond, angle, and torsional coordinates instead of a Cartesian coordinate representation. Freezing high-frequency bonds and angles in the ICMD model gives rise to constrained ICMD (CICMD) models. There are several theoretical aspects that need to be(More)
The focus of this paper is to examine whether conformational search using constrained molecular dynamics (MD) method is more enhanced and enriched toward "native-like" structures compared to all-atom MD for the protein folding as a model problem. Constrained MD methods provide an alternate MD tool for protein structure prediction and structure refinement.(More)
An efficient geometric integrator is proposed for solving the perturbed Kepler motion. This method is stable and accurate over long integration time, which makes it appropriate for treating problems in astrophysics, like solar system simulations, and atomic and molecular physics, like classical simulations of highly excited atoms in external fields. The key(More)
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