Desmond (software)
   HOME

TheInfoList



OR:

Desmond is a software package developed at
D. E. Shaw Research D. E. Shaw Research (DESRES) is a privately held biochemistry research company based in New York City. Under the scientific direction of David E. Shaw, the group's chief scientist, D. E. Shaw Research develops technologies for molecular dynami ...
to perform high-speed
molecular dynamics Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of th ...
simulations of biological systems on conventional
computer cluster A computer cluster is a set of computers that work together so that they can be viewed as a single system. Unlike grid computers, computer clusters have each node set to perform the same task, controlled and scheduled by software. The comp ...
s. The code uses novel parallel algorithms and numerical methods to achieve high performance on platforms containing multiple processors, but may also be executed on a single computer. The core and
source code In computing, source code, or simply code, is any collection of code, with or without comment (computer programming), comments, written using a human-readable programming language, usually as plain text. The source code of a Computer program, p ...
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 Commercial software, or seldom payware, is a computer software that is produced for sale or that serves commercial purposes. Commercial software can be proprietary software or free and open-source software. Background and challenge While s ...
through
Schrödinger, Inc. Schrödinger, Inc. is an international scientific software company that specializes in developing computational tools and software for drug discovery and materials science. Schrödinger's software is used by pharmaceutical companies, biotech ...


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 Ewald summation, named after Paul Peter Ewald, is a method for computing long-range interactions (e.g. electrostatic interactions) in periodic systems. It was first developed as the method for calculating electrostatic energies of ionic crystals, an ...
-based methods. 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 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 Berendsen Textile Service (formerly Sophus Berendsen, Berendsen plc and The Davis Service Group Plc) is a provider of textile maintenance services with headquarters in Søborg, Denmark. The company is a wholly owned subsidiary of French company ...
, 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. Desmond is also available in a
graphics processing unit A graphics processing unit (GPU) is a specialized electronic circuit designed to manipulate and alter memory to accelerate the creation of images in a frame buffer intended for output to a display device. GPUs are used in embedded systems, mo ...
(GPU) accelerated version that is about 60-80 times faster than the
central processing unit A central processing unit (CPU), also called a central processor, main processor or just processor, is the electronic circuitry that executes instructions comprising a computer program. The CPU performs basic arithmetic, logic, controlling, an ...
(CPU) version.


Related software tools

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 Amber is fossilized tree resin that has been appreciated for its color and natural beauty since Neolithic times. Much valued from antiquity to the present as a gemstone, amber is made into a variety of decorative objects."Amber" (2004). In M ...
and OPLS force fields, and a range of different water models. Desmond is integrated with a molecular modeling environment (Maestro, developed by
Schrödinger, Inc. Schrödinger, Inc. is an international scientific software company that specializes in developing computational tools and software for drug discovery and materials science. Schrödinger's software is used by pharmaceutical companies, biotech ...
) for setting up simulations of biological and chemical systems, and is compatible with
Visual Molecular Dynamics Visual Molecular Dynamics (VMD) is a molecular modelling and Visualization (computer graphics), visualization computer program. VMD is developed mainly as a tool to view and analyze the results of molecular dynamics simulations. It also includes ...
(VMD) for trajectory viewing and analysis.


See also

*
D. E. Shaw Research D. E. Shaw Research (DESRES) is a privately held biochemistry research company based in New York City. Under the scientific direction of David E. Shaw, the group's chief scientist, D. E. Shaw Research develops technologies for molecular dynami ...
* Folding@home * Comparison of software for molecular mechanics modeling * Metadynamics * Molecular design software *
Molecular dynamics Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of th ...


References


External links

*
Desmond Users GroupSchrödinger Desmond Product Page
{{Chemistry software Molecular dynamics software Force fields