GROMACS 3.0: a package for molecular simulation and trajectory analysis

GROMACS 3.0 is the latest release of a versatile and very well optimized pa ckage for molecular simulation. Much effort has been devoted to achieving e xtremely high performance on both workstations and parallel computers. The design includes an extraction of virial and periodic boundary conditions fr om the loops over pairwise interactions, and special software routines to e nable rapid calculation of x(-1/2). Inner loops are generated automatically in C or Fortran at compile time, with optimizations adapted to each archit ecture. Assembly loops using SSE and 3DNow! Multimedia instructions are pro vided for x86 processors, resulting in exceptional performance on inexpensi ve PC workstations. The interface is simple and easy to use (no scripting l anguage), based on standard command line arguments with self-explanatory fu nctionality and integrated documentation. All binary files are independent of hardware endian and can be read by versions of GROMACS compiled using di fferent floating-point precision. A large collection of flexible tools for trajectory analysis is included, with output in the form of finished Xmgr/G race graphs. A basic trajectory viewer is included, and several external vi sualization tools can read the GROMACS trajectory format. Starting with ver sion 3.0, GROMACS is available under the GNU General Public License from ht tp://www.gromacs.org.