OBGMX: a web-based generator of GROMACS topologies for molecular and periodic systems using the universal force field.
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 metal-organic frameworks. OBGMX is available at http://software-lisc.fbk.eu/obgmx/.
Interdisciplinary Laboratory for Computational Science (LISC). Fondazione Bruno Kessler and University of Trento, via Sommarive 18, I-38123 Povo(TN), Italy. garberoglio@fbk.eu
Giovanni
G
Garberoglio
D056004:Molecular Dynamics Simulation; D009942:Organometallic Compounds / Q000737:chemistry*; D012984:Software
D009942:Organometallic Compounds