OBGMX: A web-based generator of GROMACS topologies for molecular and periodic systems using the universal force field

被引：83

作者：

Garberoglio, Giovanni ^{[1
,2
]}

机构：

[1] Fdn Bruno Kessler, Interdisciplinary Lab Computat Sci LISC, I-38123 Povo, TN, Italy

[2] Univ Trent, I-38123 Povo, TN, Italy

来源：

JOURNAL OF COMPUTATIONAL CHEMISTRY | 2012年 / 33卷 / 27期

关键词：

molecular topologies; GROMACS; universal force field; periodic systems; metal-organic frameworks; METAL-ORGANIC FRAMEWORK; DYNAMICS SIMULATIONS; IMIDAZOLATE FRAMEWORKS; MECHANICS; PROGRAM; ALGORITHMS; PARALLEL; ENERGY;

D O I：

10.1002/jcc.23049

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

OBGMX is a web service providing topologies for the GROMACS molecular dynamics software package according to the Universal Force Field, as implemented in the Open Babel package. OBGMX can deal with molecular and periodic systems. The geometrical parameters appearing in the potential energy functions for the bonded interactions can be set to those measured in the input configuration. The performance of OBGMX in reproducing the structure of periodic systems is analyzed by calculating the root mean-squared displacements of optimized configurations of a large set of metalorganic frameworks. OBGMX is available at http://software-lisc.fbk.eu/obgmx/. (c) 2012 Wiley Periodicals, Inc.

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页码：2204 / 2208

页数：5

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