ForConX: A Forcefield Conversion Tool Based on XML

被引：7

作者：

Lesch, Volker ^{[1
]}

Diddens, Diddo ^{[1
]}

Bernardes, Carlos E. S. ^{[2
]}

Golub, Benjamin ^{[3
]}

Dequidt, Alain ^{[4
]}

Zeindlhofer, Veronika ^{[5
]}

Sega, Marcello ^{[5
,6
]}

Schroeder, Christian ^{[5
]}

机构：

[1] Westfal Wilhelms Univ Munster, Inst Phys Chem, Corrensstr 28-30, D-48149 Munster, Germany

[2] Univ Lisbon, Inst Super Tecn, Ctr Quim Estrutural, Ave Rovisco Pais, P-1049001 Lisbon, Portugal

[3] Univ Rostock, Inst Chem Phys & Theoret Chem, Dr Lorenz Weg 1, D-18059 Rostock, Germany

[4] Univ Clermont Auvergne, Inst Chim Clermont Ferrand, CNRS UMR 6296, Univ Blaise Pascal, F-63178 Aubiere, France

[5] Univ Vienna, Fac Chem, Dept Computat Biol Chem, Wahringerstr 19, A-1090 Vienna, Austria

[6] Univ Vienna, Fac Phys, Boltzmanngasse 5, A-1090 Vienna, Austria

来源：

JOURNAL OF COMPUTATIONAL CHEMISTRY | 2017年 / 38卷 / 09期

关键词：

force field; MD; force field conversion; XML; TOTAL-ENERGY CALCULATIONS; AUGMENTED-WAVE METHOD; PLANE-WAVE; SPHERICAL-HARMONICS; BASIS-SET; SOLIDS;

D O I：

10.1002/jcc.24708

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

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. (C) 2017 Wiley Periodicals, Inc.

引用

页码：629 / 638

页数：10

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