MOLSIM: A modular molecular simulation software.
(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)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/5448432
- author
- Reščič, Jurij and Linse, Per LU
- organization
- publishing date
- 2015
- 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 Inc.
- external identifiers
-
- pmid:25994597
- wos:000354886400007
- scopus:84930674394
- pmid:25994597
- 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
- 2016-04-01 14:31:00
- date last changed
- 2022-04-14 18:12:01
@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}},
keywords = {{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 Inc.}},
series = {{Journal of Computational Chemistry}},
title = {{MOLSIM: A modular molecular simulation software.}},
url = {{http://dx.doi.org/10.1002/jcc.23919}},
doi = {{10.1002/jcc.23919}},
volume = {{36}},
year = {{2015}},
}