STOCK: Structure mapper and online coarse-graining kit for molecular simulations

Bevc, Staš; Junghans, Christoph; Praprotnik, Matej

doi:10.1002/jcc.23806

Title: STOCK: Structure mapper and online coarse-graining kit for molecular simulations

Journal Article · Sun Mar 15 00:00:00 EDT 2015 · Journal of Computational Chemistry

DOI:https://doi.org/10.1002/jcc.23806· OSTI ID:1193291

Bevc, Staš ^[1]; Junghans, Christoph ^[2]; Praprotnik, Matej ^[1]

National Institute of Chemistry, Ljubljana (Slovenia)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

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.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: PHY11-25915; J1-4134; P1-0002; AC52-06NA25396

OSTI ID:: 1193291

Report Number(s):: LA-UR-14-21684; TRN: US1600425

Journal Information:: Journal of Computational Chemistry, Vol. 36, Issue 7; ISSN 0192-8651

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 9 works

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Adaptive resolution simulations of biomolecular systems Zavadlav, Julija; Bevc, Staš; Praprotnik, Matej European Biophysics Journal, Vol. 46, Issue 8 https://doi.org/10.1007/s00249-017-1248-0	journal	September 2017
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Molecular Dynamics Simulation of High Density DNA Arrays Podgornik, Rudolf; Zavadlav, Julija; Praprotnik, Matej Computation, Vol. 6, Issue 1 https://doi.org/10.3390/computation6010003	journal	January 2018
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