ForConX: A Forcefield Conversion Tool Based on XML

Author(s)
Volker Lesch, Diddo Diddens, Carlos E. S. Bernardes, Benjamin Golub, Alain Dequidt, Veronika Zeindlhofer, Marcello Sega, Christian Schroeder
Abstract

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(s)
Department of Computational Biological Chemistry, Computational and Soft Matter Physics
External organisation(s)
Universität Münster, Universidade de Lisboa, Universität Rostock, Institut de Chimie de Clermont‐Ferrand, CNRS UMR 6296
Journal
Journal of Computational Chemistry
Volume
38
Pages
629-638
No. of pages
10
ISSN
0192-8651
DOI
https://doi.org/10.1002/jcc.24708
Publication date
04-2017
Peer reviewed
Yes
Austrian Fields of Science 2012
104022 Theoretical chemistry, 103006 Chemical physics, 102009 Computer simulation
Keywords
ASJC Scopus subject areas
Computational Mathematics, General Chemistry
Portal url
https://ucrisportal.univie.ac.at/en/publications/3510c95b-2857-4406-a8e8-6ee00d30f70d