title: A Stochastic Algorithm for the Isobaric-Isothermal Ensemble with Ewald Summations for All Long Range Forces.
abstract: We present an algorithm termed COMPEL (COnstant Molecular Pressure with Ewald sum for Long range forces) to conduct simulations in the NPT ensemble. The algorithm combines novel features recently proposed in the literature to obtain a highly efficient and accurate numerical integrator. COMPEL exploits the concepts of molecular pressure, rapid stochastic relaxation to equilibrium, exact calculation of the contribution to the pressure of long-range nonbonded forces with Ewald summation, and the use of Trotter expansion to generate a robust, highly stable, symmetric, and accurate algorithm. Explicit implementation in the MOIL program and illustrative numerical examples are discussed.
authors.affiliation: Center for Theoretical Biological Physics, BioScience Research Collaborative, Rice University , Houston, Texas 77030-1402, United States.
authors.forename: Michele
authors.initials: M
authors.lastname: Di Pierro
authors.affiliation: Institute for Computational Engineering and Sciences, The University of Texas at Austin , 1 University Station A5300, Austin, Texas 78712-0165, United States.|Department of Chemistry, The University of Texas at Austin , 1 University Station A5300, Austin, Texas 78712-0165, United States.
authors.forename: Ron
authors.initials: R
authors.lastname: Elber
authors.affiliation: School of Mathematics, University of Edinburgh , James Clerk Maxwell Building, Edinburgh EH9 3FD, United Kingdom.
authors.forename: Benedict
authors.initials: B
authors.lastname: Leimkuhler
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D002712:Chlorides / Q000737:chemistry; D007477:Ions / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D012964:Sodium / Q000737:chemistry
chemical_list: D002712:Chlorides; D007477:Ions; D010455:Peptides; D012964:Sodium