What Desmond Does

Desmond can compute energies and forces for the standard fixed-charged force fields used in biomolecular simulations. A variety of integrators and support for various ensembles have been implemented in the code, including methods for thermostatting (Andersen, Nose-Hoover, and Langevin) and barostatting (Berendsen, Martyna-Tobias-Klein, and Langevin). Ensembles typically used in membrane simulations (constant surface area and surface tension) and semi-isotropic and fully anisotropic pressure coupling schemes are also available.

Desmond supports algorithms typically used to perform fast and accurate molecular dynamics. Long-range electrostatic energy and forces are calculated using particle-mesh-based Ewald techniques. Constraints, which are enforced using a variant of the SHAKE algorithm, allow the time step to be increased. These approaches can be used in combination with time-scale splitting (RESPA-based) integration schemes.

The Desmond software includes tools for minimization and energy analysis (which can be run efficiently in a parallel environment); methods for restraining atomic positions as well as molecular configurations; support for a variety of periodic cell configurations; and facilities for accurate checkpointing and restart.

Force field parameters can be assigned using an included template-based parameter assignment tool. Supported force fields include CHARMM (22,27,32,36), AMBER (94,96,99,03), and OPLS (2001,2005), as well as several in-house-developed variants (such as CHARMM22* and AMBER99SB-ILDN).

Desmond can also be used to perform absolute and relative free energy calculations. Other simulation techniques (such as replica exchange and enhanced sampling) are supported through a plug-in-based infrastructure, which also allows users to develop their own simulation algorithms and models.

Desmond is integrated with a molecular modeling environment for setting up simulations of biological and chemical systems, and is compatible with widely used tools for trajectory viewing and analysis.

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