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ForConX: A Forcefield Conversion Tool Based on XML

Autor(en)
Volker Lesch, Diddo Diddens, Carlos E. S. Bernardes, Benjamin Golub, Alain Dequidt, Veronika Zeindlhofer, Marcello Sega, Christian Schroeder
Abstrakt

The force field conversion from one MD program to another one is exhausting and error-prone. Although single conversion tools from one MD program to another exist not every combination and both directions of conversion are available for the favorite MD programs AMBER, CHARMM, DL-POLY, GROMACS, and LAMMPS. We present here a general tool for the force field conversion on the basis of an XML document. The force field is converted to and from this XML structure facilitating the implementation of new MD programs for the conversion. Furthermore, the XML structure is human readable and can be manipulated before continuing the conversion. We report, as testcases, the conversions of topologies for acetonitrile, dimethylformamide, and 1-ethyl-3-methylimidazolium trifluoromethanesulfonate comprising also Urey-Bradley and Ryckaert-Bellemans potentials.

Organisation(en)
Institut für Computergestützte Biologische Chemie, Computergestützte Physik und Physik der Weichen Materie
Externe Organisation(en)
Universität Münster, Universidade de Lisboa, Universität Rostock, Institut de Chimie de Clermont‐Ferrand, CNRS UMR 6296
Journal
Journal of Computational Chemistry
Band
38
Seiten
629-638
Anzahl der Seiten
10
ISSN
0192-8651
DOI
https://doi.org/10.1002/jcc.24708
Publikationsdatum
04-2017
Peer-reviewed
Ja
ÖFOS 2012
104022 Theoretische Chemie, 103006 Chemische Physik, 102009 Computersimulation
Schlagwörter
ASJC Scopus Sachgebiete
Computational Mathematics, Allgemeine Chemie
Link zum Portal
https://ucrisportal.univie.ac.at/de/publications/3510c95b-2857-4406-a8e8-6ee00d30f70d