A Stochastic Algorithm for the Isobaric-Isothermal Ensemble with Ewald Summations for All Long Range Forces

J Chem Theory Comput. 2015 Dec 8;11(12):5624-37. doi: 10.1021/acs.jctc.5b00648. Epub 2015 Nov 25.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Amino Acid Sequence
  • Chlorides / chemistry
  • Ions / chemistry
  • Molecular Dynamics Simulation
  • Molecular Sequence Data
  • Peptides / chemistry
  • Peptides / metabolism
  • Sodium / chemistry

Substances

  • Chlorides
  • Ions
  • Peptides
  • Sodium