Gromacs

GROMACS is a free application for molecular dynamics, simulating Newtonian equations of motion for systems of hundreds to millions of particles. It is mainly designed for biochemical molecules like lipids, nucleic acids and proteins that are made up of complicated bond interactions, but because of the application’s calculating ability including even non-bond interactions [usually dominating simulations], it is also being used in research for non-biological systems like polymers. GROMACS supports all usual algorithms for modern molecular dynamics, but it also has its standout features. It has a lot of algorithmic optimizations like the extraction of the virial calculation from innermost loops over pair interactions and the calculation of inverse square root. GROMACS has parameter files and topologies in clear text format. It performs consistency checking, and clearing of error messages. It will automatically open your compressed files through gzip upon reading. It has no scripting language, providing programs with a simple interface and command line options for output and input files. During simulation process, it will continuously update you the expected time and date of its completion. Its basic trajectory viewer only requires standard X libraries and other visualization applications can read file formats of GROMACS. Any version of GROMACS can run trajectories and input files even when compiled by a different floating-point precision. The software has fully automated topology constructor for proteins and multimeric structures. It has building blocks for 20 standard amino acid residues and modified ones, 4 deoxynucleotide and 4 nucleotide residues, sugars and lipids, special groups such as hemes and small molecules.

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