Desmond (software)
Encyclopedia
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. The code uses novel parallel algorithms and numerical techniques to achieve high performance on platforms containing a large number of processors, but may also be executed on a single computer. Desmond and its source code are available without cost for non-commercial use by universities and other not-for-profit research institutions. Desmond is available for commercial use through Schrodinger
.
Desmond can compute energies and forces 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 as well as 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. Other simulation techniques (such as replica exchange
) are supported through a plug-in-based infrastructure, which also allows users to develop their own simulation algorithms and models.
Force fields parameters can be assigned using a template-based parameter assignment tool called Viparr. Viparr currently supports several versions of the CHARMM, Amber and OPLS
force fields, as well as a range of different water model
s.
Desmond is integrated with a molecular modeling environment for setting up simulations of biological and chemical systems, and is compatible with VMD
for trajectory viewing and analysis.
D. E. Shaw Research
D. E. Shaw Research is a computational biochemistry research laboratory based in New York City. Under the scientific direction of David E. Shaw, the group's chief scientist, D. E...
to perform high-speed molecular dynamics
Molecular dynamics
Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...
simulations of biological systems on conventional computer clusters. The code uses novel parallel algorithms and numerical techniques to achieve high performance on platforms containing a large number of processors, but may also be executed on a single computer. Desmond and its source code are available without cost for non-commercial use by universities and other not-for-profit research institutions. Desmond is available for commercial use through Schrodinger
Schrodinger (company)
Schrodinger, Inc. is a company that specializes in computational drug discovery. The two main offices are in Portland, OR and New York, NY. The company makes significant contributions to the science of computational drug design, and their software is used by many pharmaceutical companies and...
.
Desmond 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-based Ewald techniques. Constraints can be enforced using the M-SHAKE algorithm. These approaches can be used in combination with time-scale splitting (RESPA-based) integration schemes.Desmond can compute energies and forces for many standard fixed-charged force fields
Force field (chemistry)
In the context of molecular modeling, a force field refers to the form and parameters of mathematical functions used to describe the potential energy of a system of particles . Force field functions and parameter sets are derived from both experimental work and high-level quantum mechanical...
used in biomolecular simulations, and is also compatible with polarizable force fields based on the Drude
Drude model
The Drude model of electrical conduction was proposed in 1900 by Paul Drude to explain the transport properties of electrons in materials...
formalism. A variety of integrators and support for various ensembles have been implemented in the code, including methods for temperature control (Andersen, Nosé-Hoover
Nosé-Hoover thermostat
The Nosé–Hoover thermostat is a deterministic method used in molecular dynamics to keep the temperature around an average. It was originally introduced by Nosé and developed further by Hoover...
, and Langevin
Langevin dynamics
In physics, Langevin dynamics is an approach to the mathematical modeling of the dynamics of molecular systems, originally developed by the French physicist Paul Langevin...
) and pressure control (Berendsen
Berendsen thermostat
The Berendsen thermostat is an algorithm to re-scale the velocities of particles in molecular dynamics simulations to control the simulation temperature.-Basic Description:In this scheme, the system is weakly coupled to a heat bath with some temperature...
, Martyna-Tobias-Klein, and Langevin). The code also supports methods for restraining atomic positions as well as 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. Other simulation techniques (such as replica exchange
Parallel tempering
Parallel tempering, also known as replica exchange MCMC sampling, is a simulation method aimed at improving the dynamic properties of Monte Carlo method simulations of physical systems, and of Markov chain Monte Carlo sampling methods more generally...
) are supported through a plug-in-based infrastructure, which also allows users to develop their own simulation algorithms and models.
Related software tools
In addition to the molecular dynamics program, the Desmond software also includes tools for minimization 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. Viparr currently supports several versions of the CHARMM, Amber and OPLS
OPLS
The OPLS force field was developed by Prof. William L. Jorgensen at Purdue University and later at Yale University.-Functional form:The functional form of the OPLS force field is very similar to that of AMBER:...
force fields, as well as a range of different water model
Water model
In computational chemistry, classical water models are used for the simulation of water clusters, liquid water, and aqueous solutions with explicit solvent. These models use the approximations of molecular mechanics...
s.
Desmond is integrated with a molecular modeling environment for setting up simulations of biological and chemical systems, and is compatible with VMD
Visual Molecular Dynamics
- External links :* * *...
for trajectory viewing and analysis.
See also
- Molecular dynamicsMolecular dynamicsMolecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...
- Software for molecular mechanics modeling
- Molecular design softwareMolecular Design softwareMolecular design software is software for molecular modeling, that provides special support for developing molecular models de novo.In contrast to the usual molecular modeling programs such as the molecular dynamics and quantum chemistry programs, such software directly supports the aspects related...
- Folding@HomeFolding@homeFolding@home is a distributed computing project designed to use spare processing power on personal computers to perform simulations of disease-relevant protein folding and other molecular dynamics, and to improve on the methods of doing so...