Desmond is a software package developed at
D. E. Shaw Research to perform high-speed
molecular dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the Motion (physics), 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 dynamics ( ...
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 newes ...
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 or source, is a plain text computer program written in a programming language. A programmer writes the human readable source code to control the behavior of a computer.
Since a computer, at base, only ...
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 ...
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. 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
In German folklore, a drude (, , pl. ''Druden'') is a kind of malevolent nocturnal spirit (an alp, kobold or hag) associated with nightmares, prevalent especially in Southern Germany. Druden were said to participate in the Wild Hunt and we ...
formalism. A variety of integrators and support for various ensembles have been implemented in the code, including methods for temperature control (
Andersen thermostat
The Andersen thermostat is a proposal in molecular dynamics simulation for maintaining constant temperature conditions. It is based on periodic reassignment of the velocities of atoms or molecules. For each atom or molecule, the reassigned velocity ...
,
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.
Desmond is also available in a
graphics processing unit
A graphics processing unit (GPU) is a specialized electronic circuit designed for digital image processing and to accelerate computer graphics, being present either as a discrete video card or embedded on motherboards, mobile phones, personal ...
(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 primary Processor (computing), processor in a given computer. Its electronic circuitry executes Instruction (computing), instructions ...
(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. Examples of it have been appreciated for its color and natural beauty since the Neolithic times, and worked as a gemstone since antiquity."Amber" (2004). In Maxine N. Lurie and Marc Mappen (eds.) ''Encyclopedia ...
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.
See also
*
Comparison of software for molecular mechanics modeling
This is a list of computer programs that are predominantly used for molecular mechanics calculations.
See also
*Car–Parrinello molecular dynamics
*Comparison of force-field implementations
*Comparison of nucleic acid simulation software
* ...
References
External links
*
Desmond Users Group(deleted)
Schrödinger Desmond Product Page
{{Chemistry software
Molecular dynamics software
Force fields (chemistry)