GROMACS
 GROMACS is a
molecular dynamics simulator, with building and analysis tools.
GROMACS is a versatile package to perform molecular dynamics,
i.e. simulate the Newtonian equations of motion for systems with
hundreds to millions of particles.
It is primarily designed for biochemical molecules like proteins and
lipids that have a lot of complicated bonded interactions, but since
GROMACS
is extremely fast at calculating the nonbonded interactions (that
usually dominate simulations) many groups are also using it for
research on non-biological systems, e.g. polymers.
It provides extremely high performance compared to other
competitors. A lot of algorithmic optimizations have been
introduced in the code. The software is normally 3-10 times faster than
any other program.
There is ongoing development to extend GROMACS with
interfaces both to Quantum Chemistry and Bioinformatics/databases.
Features include:
- 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
- There
is no scripting language - all programs use a simple interface with
command line options for input and output files
- Extensive manuals provided free of charge in electronic or
paper
format.
- Integrated graphical user interface available
for all programs
- As the simulation is proceeding,
GROMACS will continuously tell you how far it has come, and what time
and date it expects to be finished
- Both run input
files and trajectories are independent of hardware endian and can thus
be read by any version GROMACS, even if it was compiled using a
different floating-point precision. All files from GROMACS 2.0 can
further be used in the new version 3
- Write coordinates using lossy compression, which provides a
very
compact way of storing trajectory data. The accuracy can be selected by
the user
- Large selection of
flexible tools for trajectory analysis - you won't have to write any
code to perform routine analyses. The output is further provided in the
form of finished Xmgr/Grace graphs, with axis labels, legends, etc.
already in place
- A basic trajectory viewer that
only requires standard X libraries is included, and several external
visualization tools can read the GROMACS file formats
- Can be run in parallel, using standard MPI
communication
- Contains several state-of-the-art algorithms that make it
possible to
extend the time steps is simulations significantly, and thereby further
enhance performance without sacrificing accuracy or detail
- Includes a fully automated topology builder for proteins,
even
multimeric structures. Building blocks are available for the 20
standard aminoacid residues as well as some modified ones, the 4
nucleotide and 4 deoxinucleotide resides, several sugars and lipids,
and some special groups like hemes and several small molecules
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