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

doi:10.1016/0010-4655(95)00047-J

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

Laufer Center for Physical and Quantitative Biology

University of Illinois at Chicago
Hebrew University of Jerusalem
Northwestern University
Accelrys Inc.
Pfizer
Cornell University

Research output: Contribution to journal › Article › peer-review

152 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 language	English
Pages (from-to)	159-189
Number of pages	31
Journal	Computer Physics Communications
Volume	91
Issue number	1-3
DOIs	https://doi.org/10.1016/0010-4655(95)00047-J
State	Published - Sep 2 1995

Keywords

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

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10.1016/0010-4655(95)00047-J

Cite this

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title = "MOIL: A program for simulations of macromolecules",

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.",

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AU - Elber, Ron

AU - Roitberg, Adrian

AU - Simmerling, Carlos

AU - Goldstein, Robert

AU - Li, Haiying

AU - Verkhivker, Gennady

AU - Keasar, Chen

AU - Zhang, Jing

AU - Ulitsky, Alex

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AB - 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.

KW - Curve crossing

KW - Energy minimization

KW - Library of simulation programs

KW - Modeling

KW - Molecular dynamics

KW - Reaction paths

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JO - Computer Physics Communications

JF - Computer Physics Communications

IS - 1-3

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MOIL: A program for simulations of macromolecules

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Keywords

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