title: Novel procedure for thermal equilibration in molecular dynamics simulation.
abstract: 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.
authors.affiliation: Department of Chemistry, Universidad Autónoma de Coahuila, Saltillo, México.
authors.forename: Marco T
authors.initials: MT
authors.lastname: Gallo
authors.affiliation: Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, USA.
authors.forename: Barry J
authors.initials: BJ
authors.lastname: Grant
authors.affiliation: Department of Biochemistry and Cell Biology, Keck Centre for Computational Biology, Rice University, Houston, USA.
authors.forename: Miguel L
authors.initials: ML
authors.lastname: Teodoro
authors.affiliation: Department of Biochemistry and Cell Biology, Keck Centre for Computational Biology, Rice University, Houston, USA.
authors.forename: Julia
authors.initials: J
authors.lastname: Melton
authors.affiliation: Burnham Institute for Medical Research, La Jolla, USA.
authors.forename: Piotr
authors.initials: P
authors.lastname: Cieplak
authors.affiliation: Department of Biochemistry, University of Wisconsin at Madison, Madison, USA.
authors.forename: George N
authors.initials: GN
authors.lastname: Phillips
authors.affiliation: Burnham Institute for Medical Research, La Jolla, USA.
authors.forename: Boguslaw
authors.initials: B
authors.lastname: Stec
keywords: molecular dynamics; solvent coupling; thermal equilibrium