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Mol Simul. 2009 Apr 1;35(5):349-357.

Novel procedure for thermal equilibration in molecular dynamics simulation.

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Department of Chemistry, Universidad Autónoma de Coahuila, Saltillo, México.
Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, USA.
Department of Biochemistry and Cell Biology, Keck Centre for Computational Biology, Rice University, Houston, USA.
Burnham Institute for Medical Research, La Jolla, USA.
Department of Biochemistry, University of Wisconsin at Madison, Madison, USA.


We describe a simple novel procedure for achieving thermal equilibration between a protein and a surrounding solvent during molecular dynamics (MD) simulation. The method uniquely defines the length of simulation time required to achieve thermal equilibrium over a broad range of parameters, thus removing ambiguities associated with the traditional heuristic approaches. The proposed protocol saves simulation time and avoids bias introduced by the inclusion of non-equilibrium events. The key element of the procedure involves coupling only the solvent atoms to a standard heat bath. Measuring progress towards thermal equilibration involves simply monitoring the difference in temperature between the solvent and the protein. Here, we report that the results of MD simulations using the above procedure are measurably improved relative to the traditional approaches in terms of root-mean-square deviations and principal components analysis both indicating significantly less undesirable divergence.


molecular dynamics; solvent coupling; thermal equilibrium

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