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MOLSIM: A modular molecular simulation software.

Reščič, Jurij and Linse, Per LU (2015) In Journal of Computational Chemistry 36(16). p.1259-1274
Abstract
The modular software MOLSIM for all-atom molecular and coarse-grained simulations is presented with focus on the underlying concepts used. The software possesses four unique features: (1) it is an integrated software for molecular dynamic, Monte Carlo, and Brownian dynamics simulations; (2) simulated objects are constructed in a hierarchical fashion representing atoms, rigid molecules and colloids, flexible chains, hierarchical polymers, and cross-linked networks; (3) long-range interactions involving charges, dipoles and/or anisotropic dipole polarizabilities are handled either with the standard Ewald sum, the smooth particle mesh Ewald sum, or the reaction-field technique; (4) statistical uncertainties are provided for all calculated... (More)
The modular software MOLSIM for all-atom molecular and coarse-grained simulations is presented with focus on the underlying concepts used. The software possesses four unique features: (1) it is an integrated software for molecular dynamic, Monte Carlo, and Brownian dynamics simulations; (2) simulated objects are constructed in a hierarchical fashion representing atoms, rigid molecules and colloids, flexible chains, hierarchical polymers, and cross-linked networks; (3) long-range interactions involving charges, dipoles and/or anisotropic dipole polarizabilities are handled either with the standard Ewald sum, the smooth particle mesh Ewald sum, or the reaction-field technique; (4) statistical uncertainties are provided for all calculated observables. In addition, MOLSIM supports various statistical ensembles, and several types of simulation cells and boundary conditions are available. Intermolecular interactions comprise tabulated pairwise potentials for speed and uniformity and many-body interactions involve anisotropic polarizabilities. Intramolecular interactions include bond, angle, and crosslink potentials. A very large set of analyses of static and dynamic properties is provided. The capability of MOLSIM can be extended by user-providing routines controlling, for example, start conditions, intermolecular potentials, and analyses. An extensive set of case studies in the field of soft matter is presented covering colloids, polymers, and crosslinked networks. © 2015 Wiley Periodicals, Inc. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
molecular simulation, software, coarse-grained model, all-atom model, Monte Carlo simulation, molecular dynamics, Brownian dynamics, ensembles, boundary conditions, Ewald sum
in
Journal of Computational Chemistry
volume
36
issue
16
pages
1259 - 1274
publisher
John Wiley & Sons
external identifiers
  • pmid:25994597
  • wos:000354886400007
  • scopus:84930674394
ISSN
1096-987X
DOI
10.1002/jcc.23919
language
English
LU publication?
yes
id
3d956d55-b2c6-41a8-ba4f-51f7bf3c853d (old id 5448432)
date added to LUP
2015-06-23 17:39:47
date last changed
2017-08-27 04:54:46
@article{3d956d55-b2c6-41a8-ba4f-51f7bf3c853d,
  abstract     = {The modular software MOLSIM for all-atom molecular and coarse-grained simulations is presented with focus on the underlying concepts used. The software possesses four unique features: (1) it is an integrated software for molecular dynamic, Monte Carlo, and Brownian dynamics simulations; (2) simulated objects are constructed in a hierarchical fashion representing atoms, rigid molecules and colloids, flexible chains, hierarchical polymers, and cross-linked networks; (3) long-range interactions involving charges, dipoles and/or anisotropic dipole polarizabilities are handled either with the standard Ewald sum, the smooth particle mesh Ewald sum, or the reaction-field technique; (4) statistical uncertainties are provided for all calculated observables. In addition, MOLSIM supports various statistical ensembles, and several types of simulation cells and boundary conditions are available. Intermolecular interactions comprise tabulated pairwise potentials for speed and uniformity and many-body interactions involve anisotropic polarizabilities. Intramolecular interactions include bond, angle, and crosslink potentials. A very large set of analyses of static and dynamic properties is provided. The capability of MOLSIM can be extended by user-providing routines controlling, for example, start conditions, intermolecular potentials, and analyses. An extensive set of case studies in the field of soft matter is presented covering colloids, polymers, and crosslinked networks. © 2015 Wiley Periodicals, Inc.},
  author       = {Reščič, Jurij and Linse, Per},
  issn         = {1096-987X},
  keyword      = {molecular simulation,software,coarse-grained model,all-atom model,Monte Carlo simulation,molecular dynamics,Brownian dynamics,ensembles,boundary conditions,Ewald sum},
  language     = {eng},
  number       = {16},
  pages        = {1259--1274},
  publisher    = {John Wiley & Sons},
  series       = {Journal of Computational Chemistry},
  title        = {MOLSIM: A modular molecular simulation software.},
  url          = {http://dx.doi.org/10.1002/jcc.23919},
  volume       = {36},
  year         = {2015},
}