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GROMACS is a versatile package to perform molecular dynamics for systems with hundreds to millions of particles. |
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- GROMACS provides extremely high performance compared to all other programs.
- GROMACS can make simultaneous use of both CPU and GPU available in a system. There are options to statically and dynamically balance the load between the different resources.
- GROMACS is user-friendly, with topologies and parameter files written in clear text format.
- Both run input files and trajectories are independent of hardware endian-ness, and can thus be read by any version GROMACS.
- GROMACS comes with a large selection of flexible tools for trajectory analysis.
- GROMACS can be run in parallel, using the standard MPI communication protocol.
- GROMACS contains several state-of-the-art algorithms.
- GROMACS is Free Software, available under the GNU Lesser General Public License (LGPL).
Weaknesses
- GROMACS does not do to much further analysis to get very high simulation speed.
- Sometimes it is challenging to get non-standard information about the simulated system.
- Different versions sometimes have differences in default parameters/methods. Reproducing older version simulations with a newer version can be difficult.
- Additional tools and utilities provided by GROMACS are sometimes not the top quality.
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Analyzing results
GROMACS Tools
GROMACS contains many tools that for analysing your results such as read trajectories (XTC, TNG or TRR format) as well as a coordinate file (GRO, PDB, TPR) and write plots in the XVG format. A list of commands with a short description can be find organised by topic at the official website.
VMD
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting, it is free of charge, and includes source code.
Useful links
- GROMACS Manuals and documentation
- GROMACS Community Forums
- Useful MD Tutorials for GROMACS
- VMD Visual Molecular Dynamics