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GROMOS


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OS: Linux, ...



Methods: MD


Features:

GROMOS can perform energy minimization and molecular dynamics simulation (constant energy or temperature, constant volume or pressure), in vacuo, in crystals or in aqueous or any other solution. Molecular conformation as a function of the type of environment can be studied.

The quantum-mechanical equilibrium properties of a molecular system can be studied using path-integral simulation.

A number of techniques to efficiently search conformational space for low energy conformations can be used: simulation in 4 spatial dimensions, soft-core non-bonded interaction, local-elevation search, stochastic dynamics simulation.

Long-range forces can be handled by an efficient twin-range method, and long-range electrostatic forces approximated by a Poisson-Boltzmann reaction field force.

Special (non-physical) forces can be applied to restrain the molecular system: position restraining of atoms; atom-atom distance restraining, useful when refining spatial molecular structure on the basis of NMR (NOE) data; J-coupling constant restraining, useful when refining spatial molecular structure on the basis of NMR (J-value) data; dihedral-angle restraining, useful when performing umbrella sampling;

Free energy differences between different states of a molecular system can be calculated using a variety of methods: thermodynamic integration (slow growth or numerical quadrature), one step extrapolation based on the perturbation formula or a Taylor expansion of the free energy. The Hamiltonian is made a function of two parameters, l and u. The former controls the change of atom mass, non-bonded interaction type, charge, etc., of bond lengths, bond angles and dihedral angles. The latter controls the coupling between the 4-th dimension and the first 3 dimensions in a 4D-MD simulation. This option yields the opportunity to calculate binding constants for host-guest systems.

Vectorised non-bonded interaction subroutines are available for Cray computers, and parallelised ones for Silicon Graphics multi-processor machines.

GROMOS contains a number of programs for analysing structures and simulation trajectories.

The file structure of GROMOS has been modified (compared to GROMOS87) such that it is easy to interface GROMOS to other scientific programs and to add functionality. Reading of GROMOS87 files is not possible anymore.

GROMOS96 comes with 60 examples (command-, input- and output files) covering the most important applications of all 40 programs.

It also comes with the latest versions of the GROMOS force fields, the general 43A1 force field, and the 43B1 force field for simulation of isolated molecules.

It also comes with the GROMOS96 manual and users guide (1042 pages), which is not a "do this, do that" manual, but much more. It describes the algorithms for molecular simulation as implemented in GROMOS together with a host of technical background information. The GROMOS file structure is described in order to allow for interfacing to other programs and data. A complete specification of the current GROMOS interaction function for biomolecular simulation is provided. The about 60 tutorial examples are described, and guidelines for modification of programs and data are given.


Link: http://www.igc.ethz.ch/GROMOS/index


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