Frequently asked questions

  1. Can you please make a topology for my molecule Short answer: No. Longer answer: in the not so far future we plan to build an automatic service for this purpose at this website.

  2. Can you add topologies in force field X or Y? Short answer: No. Longer answer: We may add support for the Charmm generalized force field, but don't hold your breath. We also plan to add new force fields.

  3. Can you convert the input file to package W or Z? No. This is done better by other groups who specialize in those packages.

  4. How do I cite the topologies/structures provided here in my paper? Easy. The references you need are [1] and [2], and possibly others as indicated on the specific molecule pages.

  5. Can I cite this website or paper [1] as a source of experimental data? We knew you'd ask this. NO!!! It is bad enough to cite a handbook rather than the original source, never cite a theoretical paper for an experimental number, but please see the next question ...

  6. ... but you refer to [1] for experimental numbers yourself. ¿Qué? Ah, well spotted. This is because in [1] we provide new interpolations of existing experimental data. These are described in the paper. Please cite both [1] and the data our interpolation was based upon, details are in the supporting information to our paper.

  7. Can I contribute molecules to this website? We thought you'd never ask! Yes that is possible. For now we will only accept contributions of GAFF [3] or OPLS/AA [4] molecules if most of the liquid properties have been evaluated and the results have been published. If we do add your models they will be properly referenced of course.

  8. Can I contribute results for a different force field to this website? Yes that is possible. In this case you should cover a large fraction of the molecules in the database, compute most of the properties, publish the results, and send us all the GROMACS input files. Of course you will be credited appropriately.

  9. Can I contribute results for different properties to this website? Yes: you should cover a large fraction of the molecules in the database, compute the new properties, publish the results, and send us the relevant GROMACS input files plus the simulated and experimental properties, fully referenced. You will be credited appropriately.

  10. Can I help with the maintainance of this website? Thanks for the offer but that won't be needed right now, unless you intend to contribute a lot of data.

  11. Why is my back button in Chrome not working for the correlationplot? Unfortunately, Chrome doesn't have a page cache. So you have to recalibrate your plot every time you're using Chrome's back button. It's annoying, we know, but you can always try a different browser. Firefox is working!


References

  1. 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. Theor. Comput. 8, 61-74 (2012). DOI
  2. David van der Spoel and Paul J. van Maaren and Carl Caleman GROMACS Molecule & Liquid Database, Bioinformatics 28, 752-753 (2012). DOI
  3. 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).
  4. 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).