On Sun, 25 Dec 2011 20:45:44 +0000 (GMT) Lara Bunte <lara.bu...@yahoo.de> wrote: > Hello > > I have a few questions about molecular dynamics simulations. > > 1) For a molecule Newton's equation of motion is solved. Do I get > here one resulting force for the hole molecule or do I get a lot of > forces, one for each atom?
YMMV. If you're using an united atom force field, e.g. the methyl groups (CH3) will be represented as a single fictitious atom. If, on the other hand you're using an all-atom force field every atom will be present explicitly in the calculation and you will get forces for every one of them. Some force fields even have more fictitious particles than physical atoms; e.g. the tip4p force field for water is a four-site model that includes a dummy atom. > 2) The force is calculated from the potential. This consists of the > sum of potentials linear vibration, oscillation angle, torsional and > non-binding parts as Coulomb and Lennard-Jones potential. > > How do you calculate the parameters for these potentials? I heard > something about QM calculations but what do they how calculate? You can obtain parameters either directly from experiment (may be nontrivial) or from high-level QM calculations, or indirectly by fitting the parameters in order to reproduce the experimental values for quantities such as particle densities and radial distribution functions. In QM calculations one basically solves the Schrödinger (or Dirac) equation that describes the behavior of electrons, which are responsible for practically all of the properties of "normal" matter. You can find more by googling about quantum chemistry. The construction of force fields is, however, somewhat of a black art. It is perfectly possible to construct a seemingly sensible force field that ends up giving bad results. -- -------------------------------------------------------- Mr. Jussi Lehtola, M. Sc. Doctoral Student jussi.leht...@helsinki.fi Department of Physics http://www.helsinki.fi/~jzlehtol University of Helsinki Office phone: +358 9 191 50 632 Finland -------------------------------------------------------- Jussi Lehtola, FM Tohtorikoulutettava jussi.leht...@helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto Työpuhelin: (0)9 191 50 632 -------------------------------------------------------- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
