GROMACS: fast, flexible, and free

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.     

Water Relaxation Measurements on Semiquinones of Various Flavoproteins

The water relaxation rates of several flavoproteins in the semiquinone state have been investigated by the spin echo technique. The results indicate a rather unspecific interaction between water and the protein-bound flavosemiquinones. An average interaction distance of 0.3-0.5 nm has been estimated. From the temperature dependence of the rate constants the free energy of activation for proton exchange is calculated to be about 17 kJ/mol. The rate of proton exchange is around 10¹¹ s?¹ for the flavosemiquinones investigated are accessible to water regardless of their ionic state. The large difference in relaxation rates of water protons between D - and L - amino-acid oxidases is noticeable. Oxynitrilase exhibits the highest whereas Azotobacter vinelandii flavodoxin shows the lowest water relaxation rate of the flavoproteins studied. The results are discussed in relation to the visible-light absorption properties of the flavoproteins.     

Approach to nonadiabatic transitions by density matrix evolution and molecular dynamics simulations

Many biological processes are characterized by an essentially quantum dynamical event, such as electron or proton transfer, in a complex classical environment. To treat such processes properly by computer simulation, allowing nonadiabatic transitions involving excited states, we recently developed a density matrix evolution (DME ) method [H. J. C. Berendsen and J. Mavri, J. Phys. Chem, 97 , 13464 (1993)] which simulates the dynamics of quantum systems embedded in a classical environment. The formalism of the method is presented and an overview of the applications ranging from collisions of a quantum harmonic oscillator with noble gas atoms to proton tunneling in a double-well hydrogen bond is given. The methodology for treatment of proton-transfer processes with inclusion of excited states is presented. Future application of the method on biologically interesting processes, such as proton transfer in enzymatic reactions, is discussed. © 1996 John Wiley & Sons, Inc.