STOCK: Structure mapper and online coarse-graining kit for molecular simulations
Abstract
We present a web toolkit STructure mapper and Online Coarse-graining Kit for setting up coarse-grained molecular simulations. The kit consists of two tools: structure mapping and Boltzmann inversion tools. The aim of the first tool is to define a molecular mapping from high, e.g. all-atom, to low, i.e. coarse-grained, resolution. Using a graphical user interface it generates input files, which are compatible with standard coarse-graining packages, e.g. VOTCA and DL_CGMAP. Our second tool generates effective potentials for coarse-grained simulations preserving the structural properties, e.g. radial distribution functions, of the underlying higher resolution model. The required distribution functions can be provided by any simulation package. Simulations are performed on a local machine and only the distributions are uploaded to the server. The applicability of the toolkit is validated by mapping atomistic pentane and polyalanine molecules to a coarse-grained representation. Effective potentials are derived for systems of TIP3P (transferable intermolecular potential 3 point) water molecules and salt solution. The presented coarse-graining web toolkit is available at http://stock.cmm.ki.si.
- Authors:
-
- National Institute of Chemistry, Ljubljana (Slovenia)
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Publication Date:
- Research Org.:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1193291
- Report Number(s):
- LA-UR-14-21684
Journal ID: ISSN 0192-8651; TRN: US1600425
- Grant/Contract Number:
- PHY11-25915; J1-4134; P1-0002; AC52-06NA25396
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Computational Chemistry
- Additional Journal Information:
- Journal Volume: 36; Journal Issue: 7; Journal ID: ISSN 0192-8651
- Publisher:
- Wiley
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 74 ATOMIC AND MOLECULAR PHYSICS; 97 MATHEMATICS AND COMPUTING; coarse-graining; molecular simulations; iterative Boltzmann; structure mapping; web tool
Citation Formats
Bevc, Staš, Junghans, Christoph, and Praprotnik, Matej. STOCK: Structure mapper and online coarse-graining kit for molecular simulations. United States: N. p., 2015.
Web. doi:10.1002/jcc.23806.
Bevc, Staš, Junghans, Christoph, & Praprotnik, Matej. STOCK: Structure mapper and online coarse-graining kit for molecular simulations. United States. https://doi.org/10.1002/jcc.23806
Bevc, Staš, Junghans, Christoph, and Praprotnik, Matej. Sun .
"STOCK: Structure mapper and online coarse-graining kit for molecular simulations". United States. https://doi.org/10.1002/jcc.23806. https://www.osti.gov/servlets/purl/1193291.
@article{osti_1193291,
title = {STOCK: Structure mapper and online coarse-graining kit for molecular simulations},
author = {Bevc, Staš and Junghans, Christoph and Praprotnik, Matej},
abstractNote = {We present a web toolkit STructure mapper and Online Coarse-graining Kit for setting up coarse-grained molecular simulations. The kit consists of two tools: structure mapping and Boltzmann inversion tools. The aim of the first tool is to define a molecular mapping from high, e.g. all-atom, to low, i.e. coarse-grained, resolution. Using a graphical user interface it generates input files, which are compatible with standard coarse-graining packages, e.g. VOTCA and DL_CGMAP. Our second tool generates effective potentials for coarse-grained simulations preserving the structural properties, e.g. radial distribution functions, of the underlying higher resolution model. The required distribution functions can be provided by any simulation package. Simulations are performed on a local machine and only the distributions are uploaded to the server. The applicability of the toolkit is validated by mapping atomistic pentane and polyalanine molecules to a coarse-grained representation. Effective potentials are derived for systems of TIP3P (transferable intermolecular potential 3 point) water molecules and salt solution. The presented coarse-graining web toolkit is available at http://stock.cmm.ki.si.},
doi = {10.1002/jcc.23806},
journal = {Journal of Computational Chemistry},
number = 7,
volume = 36,
place = {United States},
year = {Sun Mar 15 00:00:00 EDT 2015},
month = {Sun Mar 15 00:00:00 EDT 2015}
}
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