Deutsch
 
Hilfe Datenschutzhinweis Impressum
  DetailsucheBrowse

Datensatz

 
 
DownloadE-Mail
  Enabling grand-canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module.

Pool, R., Heringa, J., Höfling, M., Schulz, R., Smith, J. C., & Feenstra, K. A. (2012). Enabling grand-canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module. Journal of Computational Chemistry, 33(12), 1207-1214. doi:10.1002/jcc.22947.

Item is

Dateien

einblenden: Dateien
ausblenden: Dateien
:
2056282.pdf (Verlagsversion), 1020KB
Name:
2056282.pdf
Beschreibung:
-
OA-Status:
Sichtbarkeit:
Öffentlich
MIME-Typ / Prüfsumme:
application/pdf / [MD5]
Technische Metadaten:
Copyright Datum:
-
Copyright Info:
-
Lizenz:
-

Externe Referenzen

einblenden:
ausblenden:
Beschreibung:
-
OA-Status:

Urheber

einblenden:
ausblenden:
 Urheber:
Pool, R., Autor
Heringa, J., Autor
Höfling, M.1, Autor           
Schulz, R., Autor
Smith, J. C., Autor
Feenstra, K. A., Autor
Affiliations:
1Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society, ou_578631              

Inhalt

einblenden:
ausblenden:
Schlagwörter: grand-canonical Monte Carlo; GROMACS; python; API; trajectory analysis
 Zusammenfassung: We report on a python interface to the GROMACS molecular simulation package, GromPy (available at https://github.com/GromPy). This application programming interface (API) uses the ctypes python module that allows function calls to shared libraries, for example, written in C. To the best of our knowledge, this is the first reported interface to the GROMACS library that uses direct library calls. GromPy can be used for extending the current GROMACS simulation and analysis modes. In this work, we demonstrate that the interface enables hybrid Monte-Carlo/molecular dynamics (MD) simulations in the grand-canonical ensemble, a simulation mode that is currently not implemented in GROMACS. For this application, the interplay between GromPy and GROMACS requires only minor modifications of the GROMACS source code, not affecting the operation, efficiency, and performance of the GROMACS applications. We validate the grand-canonical application against MD in the canonical ensemble by comparison of equations of state. The results of the grand-canonical simulations are in complete agreement with MD in the canonical ensemble. The python overhead of the grand-canonical scheme is only minimal.

Details

einblenden:
ausblenden:
Sprache(n): eng - English
 Datum: 2012-02-282012-05-05
 Publikationsstatus: Erschienen
 Seiten: -
 Ort, Verlag, Ausgabe: -
 Inhaltsverzeichnis: -
 Art der Begutachtung: Expertenbegutachtung
 Identifikatoren: DOI: 10.1002/jcc.22947
 Art des Abschluß: -

Veranstaltung

einblenden:

Entscheidung

einblenden:

Projektinformation

einblenden:

Quelle 1

einblenden:
ausblenden:
Titel: Journal of Computational Chemistry
Genre der Quelle: Zeitschrift
 Urheber:
Affiliations:
Ort, Verlag, Ausgabe: -
Seiten: - Band / Heft: 33 (12) Artikelnummer: - Start- / Endseite: 1207 - 1214 Identifikator: -