GROMAC Information

GROMACS provides extremely high performance compared to all other programs. A lot of algorithmic optimizations have been introduced in the code; we have for instance extracted the calculation of the virial from the innermost loops over pairwise interactions, and we use our own software routines to calculate the inverse square root. The innermost loops are generated automatically in either C or Fortran at compile time, with optimizations adopted to your architecture. Assembly loops using SSE and 3DNow! multimedia instructions are provided for i386 processors, separate versions using all x86-64 registers are used on Opteron x86-64 and Xeon EM64t machines. This results in exceptional performance on inexpensive PC workstations, and for Pentium IV/Opteron processors there are also SSE2 double precision assembly loops. There are new manually tuned assembly loops for ia64 (both single and double precision), and last but certainly not least we have written Altivec assembly loops both for Linux and Mac OS X. Gromacs is normally 3-10 timesfaster than any other program; check the article in Journal of Molecular Modeling (reference can be found under resources) for a comparison benchmark. GROMACS is user-friendly, with topologies and parameter files written in clear text format. There is a lot of consistency checking, and clear error messages are issued when something is wrong. Since the C preprocessor is used, you can have conditional parts in your topologies and include other files. You can even compress most files and GROMACS will automatically pipe them through gzip upon reading. There is no scripting language - all programs use a simple interface with command line options for input and output files. You can always get help on the options by using the -h option, or use the extensive manuals provided free of charge in electronic or paper format. There is also an integrated graphical user interface available for all programs. As the simulation is proceeding, GROMACS will continuously tell you how far it has come, and ...