MOIL: A program for simulations of macromolecules

Ron Elber, Adrian Roitberg, Carlos Simmerling, Robert Goldstein, Haiying Li, Gennady Verkhivker, Chen Keasar, Jing Zhang, Alex Ulitsky

Research output: Contribution to journalArticlepeer-review

148 Scopus citations

Abstract

A package of computer programs for molecular dynamics simulations-MOIL-is described. A flexible data structure enables the study of macromolecules with potentials consistent with the AMBER/OPLS force field. The supplied parameter set has proteins in mind. In addition to 'wide spread' applications such as energy, energy minimization, normal modes, dynamics and free energy calculations code is also provided to pursue less common applications. This includes reaction path calculations (in condensed phases), uses of the mean field approach for enhanced sampling (LES-locally enhanced sampling) and calculations of curve crossing using the Landau-Zener model. A brief review of the overall program is provided. A few modules are discussed in considerable detail.

Original languageEnglish
Pages (from-to)159-189
Number of pages31
JournalComputer Physics Communications
Volume91
Issue number1-3
DOIs
StatePublished - 2 Sep 1995
Externally publishedYes

Keywords

  • Curve crossing
  • Energy minimization
  • Library of simulation programs
  • Modeling
  • Molecular dynamics
  • Reaction paths

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