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In general, a simulation requires three different types of information:

Description of the interaction energy terms
Description of the molecules in the system
Description of the boundary conditions.

Simulaid will help in various aspects of establishing these. In order to help clarify the various functionalities of Simulaid, a brief description is given of the various components of these descriptions. Frequent reference will be made to the PDB (Protein Data Bank) format that is considered the 'lingua franca' of molecular simulations (although it has a number of 'dialects') and to formats used by the simulation packages Amber, Charmm, Gromos/Gromacs, Discover, Macromodel, and MMC.