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Desmond  
 
Desmond
Description 
Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms containing a large number of processors, but may also be executed on a single computer.

Desmond can compute energies and forces for many standard fixed-charged force fields used in biomolecular simulations, the parameters for which can be assigned using a template-based parameter assignment tool. Desmond 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 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.
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.

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.

Official Homepage
      
Documentation
Users Manual
User Manual (PDF)
Tutorial (PDF)

License Agreement and Citation Format
Citation Format 
LICENSEE agrees to acknowledge the use of the SOFTWARE in any reports or publications of results obtained with the SOFTWARE as follows:

"Desmond Molecular Dynamics System, version X.Y, D. E. Shaw Research, New York, NY."

Where ’X’ and ’Y’ are to be replaced with the major- and minor-release number of the version used in the published research.  If the published research isbased on results obtained with any Software Modification or any complementary code not developed by DESRES, then those variants must be acknowledged assuch.  

LICENSEE is also requested to include a citation to the following paper:

"K. J. Bowers, E. Chow, H. Xu, R. O. Dror, M. P. Eastwood, B. A. Gregersen, J. L. Klepeis, I. Kolossvry, M. A. Moraes, F. D. Sacerdoti, J. K. Salmon, Y. Shan, and D. E. Shaw.  Scalable algorithms for molecular dynamics simulations on commodity clusters.  Proceedings of the 2006 ACM/IEEE Conference on Supercomputing (SC06), Tampa, FL, 11 to 17 November 2006 (ACM Press, New York, 2006)."

How to Access the Program 
 
Availability
Server Version Path Parallelization Methods
Axle 3.0.1.1 /apps/Desmond/Desmond_Maestro_2011 MPI
Using the Program
 
Additional Notes
 
Last Updated - 5th Oct 2011
 
     
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