Desmond is a software package developed at
D. E. Shaw Research to perform high-speed
molecular dynamics simulations of biological systems on conventional
computer clusters.[1][2][3][4] The code uses novel parallel algorithms[5] and numerical methods[6] to achieve high performance on platforms containing multiple processors,[7] but may also be executed on a single computer.
The core and
source code are available at no cost for non-commercial use by universities and other not-for-profit research institutions, and have been used in the
Folding@home distributed computing project. Desmond is available as
commercial software through
Schrödinger, Inc.
Molecular dynamics program
Desmond supports algorithms typically used to perform fast and accurate molecular dynamics. Long-range electrostatic energy and forces can be calculated using
particle mesh Ewald-based methods.[8][9] Constraints can be enforced using the
M-SHAKE algorithm. These methods can be used together with time-scale splitting (RESPA-based) integration schemes.
Desmond can compute energies and forces[10] for many standard fixed-charged
force fields used in biomolecular simulations, and is also compatible with polarizable force fields based on the
Drude formalism. A variety of integrators and support for various ensembles have been implemented in the code, including methods for temperature control (Andersen,
Nosé-Hoover, and
Langevin) and pressure control (
Berendsen, Martyna-Tobias-Klein, and Langevin). The code also supports methods for restraining atomic positions and molecular configurations; allows simulations to be carried out using a variety of periodic cell configurations; and has facilities for accurate checkpointing and restart.
Desmond can also be used to perform absolute and relative free energy calculations (e.g.,
free energy perturbation). Other simulation methods (such as
replica exchange) are supported through a plug-in-based infrastructure, which also allows users to develop their own simulation algorithms and models.
Along with the molecular dynamics program, the Desmond software also includes tools for minimizing and energy analysis, both of which can be run efficiently in a parallel environment.
Force fields parameters can be assigned using a template-based parameter assignment tool called Viparr. It currently supports several versions of the
CHARMM,
Amber and
OPLS force fields, and a range of different
water models.
Desmond is integrated with a molecular modeling environment (Maestro, developed by
Schrödinger, Inc.) for setting up simulations of biological and chemical systems, and is compatible with
Visual Molecular Dynamics (VMD) for trajectory viewing and analysis.
^
Edmond Chow; Charles A. Rendleman; Kevin J. Bowers; Ron O. Dror; Douglas H. Hughes; Justin Gullingsrud; Federico D. Sacerdoti; David E. Shaw (July 2008).
"Desmond Performance on a Cluster of Multicore Processors". D. E. Shaw Research Technical Report DESRES/TR--2008-01. {{
cite journal}}: Cite journal requires |journal= (
help)
^
Shan, Yibing; Klepeis, John L.; Eastwood, Michael P.; Dror, Ron O.; Shaw, David E. (2005). "Gaussian split Ewald: A fast Ewald mesh method for molecular simulation". The Journal of Chemical Physics. 122 (5): 054101.
Bibcode:
2005JChPh.122e4101S.
doi:
10.1063/1.1839571.
PMID15740304.
S2CID35865319.