Compound Database

The compounds are listed with their systematic names (IUPAC), an alternative name, their Chemical Abstracts Service registry number (CAS), ChemSpider ID (CSID) and formula. A full description of how the topologies were generated and how the physical properties are calculated can be found in ref. 2 (available for download here).

The force fields used for the benchmark underlying part of this website [2,3], were the Generalized Amber force field (GAFF)[4] and the Optimized Potential for Liquid Simulations for all atoms (OPLS/AA)[5]. More information on these force fields can be found the references and on their respective websites (click on Links).

We kindly ask that you cite our papers [2,3] if you use the models from this website in your own scientific publications.

1. Berk Hess and Carsten Kutzner and David van der Spoel and Erik Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation, J. Chem. Theory Comput. 4, 435-447 (2008). DOI
2. Carl Caleman and Paul J. van Maaren and Minyan Hong and Jochen S. Hub and Luciano T. Costa and David van der Spoel Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant, J. Chem. Theory Comput. 8, 61-74 (2012). DOI
3. David van der Spoel and Paul J. van Maaren and Carl Caleman GROMACS Molecule & Liquid Database, Bioinformatics 28, 752-753 (2012). DOI
4. J. Wang and R. M. Wolf and J. W. Caldwell and P. A. Kollman and D. A. Case Development and testing of a general AMBER force field, J. Comp. Chem. 25, 1157-1174 (2004).
5. William L. Jorgensen and Julian Tirado-Rives Potential energy functions for atomic-level simulations of water and organic and biomolecular systems, Proc. Natl. Acad. Sci. U.S.A. 102, 6665-6670 (2005).