New functionalities in the GROMOS biomolecular simulation software
| Autor: | Sereina Riniker, Jane R. Allison, Daan P. Geerke, Nathan Schmid, Philippe H. Hünenberger, Bruno A. C. Horta, Wilfred F. van Gunsteren, Anna-Pitschna E. Kunz |
|---|---|
| Přispěvatelé: | Molecular and Computational Toxicology, AIMMS |
| Jazyk: | angličtina |
| Rok vydání: | 2012 |
| Předmět: |
SDG 16 - Peace
Non-equilibrium thermodynamics Molecular Dynamics Simulation 010402 general chemistry computer.software_genre 01 natural sciences Force field (chemistry) Molecular dynamics Polarizability 0103 physical sciences Computer Simulation Statistical physics Adiabatic process 010304 chemical physics Chemistry Viscosity SDG 16 - Peace Justice and Strong Institutions Solvation General Chemistry Models Theoretical Justice and Strong Institutions 0104 chemical sciences Simulation software Computational Mathematics Granularity computer |
| Zdroj: | Journal of Computational Chemistry, 33(3), 340-353. John Wiley and Sons Inc. Kunz, A P E, Allison, J R, Geerke, D P, Horta, B A C, Hünenberger, P H, Riniker, S, Schmid, N & van Gunsteren, W F 2012, ' New functionalities in the GROMOS biomolecular simulation software ', Journal of Computational Chemistry, vol. 33, no. 3, pp. 340-353 . https://doi.org/10.1002/jcc.21954 Journal of Computational Chemistry |
| ISSN: | 0192-8651 |
| DOI: | 10.1002/jcc.21954 |
| Popis: | Since the most recent description of the functionalities of the GROMOS software for biomolecular simulation in 2005 many new functions have been implemented. In this article, the new functionalities that involve modified forces in a molecular dynamics (MD) simulation are described: the treatment of electronic polarizability, an implicit surface area and internal volume solvation term to calculate interatomic forces, functions for the GROMOS coarse-grained supramolecular force field, a multiplicative switching function for nonbonded interactions, adiabatic decoupling of a number of degrees of freedom with temperature or force scaling to enhance sampling, and nonequilibrium MD to calculate the dielectric permittivity or viscosity. Examples that illustrate the use of these functionalities are given. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2012 |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|
Plný text