PloS one, 2015-07, Vol.10 (7), p.e0131754-e0131754
2015
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Details
- Autor(en) / Beteiligte
- Titel
- Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA
- Ist Teil von
- PloS one, 2015-07, Vol.10 (7), p.e0131754-e0131754
- Ort / Verlag
- United States: Public Library of Science
- Erscheinungsjahr
- 2015
- Quelle
- MEDLINE
- Beschreibungen/Notizen
- We discuss recent advances of the VOTCA package for systematic coarse-graining. Two methods have been implemented, namely the downhill simplex optimization and the relative entropy minimization. We illustrate the new methods by coarse-graining SPC/E bulk water and more complex water-methanol mixture systems. The CG potentials obtained from both methods are then evaluated by comparing the pair distributions from the coarse-grained to the reference atomistic simulations. In addition to the newly implemented methods, we have also added a parallel analysis framework to improve the computational efficiency of the coarse-graining process.
- Sprache
- Englisch
- Identifikatoren
- ISSN: 1932-6203eISSN: 1932-6203DOI: 10.1371/journal.pone.0131754Titel-ID: cdi_plos_journals_1698374405
- Format
- –
- Schlagworte
- Algorithms, ATOMIC AND MOLECULAR PHYSICS, Computational chemistry, Computer applications, Computer simulation, Computing time, Entropy, Granulation, methanol, Methanol - chemistry, Molecular Conformation, Molecular Dynamics Simulation, Open source software, Optimization, Physical chemistry, Physics, potential energy, reflection, simulation and modeling, thermodynamics, Time Factors, Water - chemistry