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Desmond

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Desmond: High-Performance Molecular Dynamics Simulations for Biomolecular Systems

Desmond's combined speed and accuracy make possible long time scale molecular dynamics simulations, allowing users to examine events of great biological and pharmaceutical importance. Seamlessly integrated with Maestro, Desmond provides comprehensive setup, simulation, and analysis tools.

The Advantages of Molecular Dynamics Simulations

Biological systems are dynamic in nature; analyzing their motion at the molecular and atomistic level is therefore essential to understanding key biological phenomena. For decades, there has been keen interest in modeling the dynamic aspects of protein structure and function, and molecular dynamics (MD) simulation stands alone as the fundamental computational tool for capturing dynamic events of scientific interest and pharmaceutical relevance. More recently, static structure-based approaches, such as docking and virtual screening, have made important strides in advancing drug discovery. MD, especially when coupled with these other computational tools, will open the door to addressing the many drug discovery problems for which the dynamic nature of proteins cannot be ignored, as in the mechanisms of highly mobile membrane proteins and in ligand-induced conformational changes of active sites.

Many biological phenomena of scientific and pharmaceutical interest occur on time scales that are computationally demanding to simulate. A high-performance MD code, together with continuously advancing computer hardware technologies, can be used to perform simulations on time scales that illuminate these important biological processes. Desmond, a newly developed MD code created by D. E. Shaw Research, provides an unprecedented combination of parallel scalability, simulation throughput, and scientific accuracy to achieve these goals.

Evaluation Copies

While Schrödinger will be distributing Desmond for commercial use, Desmond is available without cost for non-commercial use by universities and other not-for-profit research institutions from D. E. Shaw Research. Please click here to visit the D. E. Shaw Research website for information on how to obtain Desmond.

For all commercial users, to request an evaluation copy of Desmond, please contact us via the Sales Center . Our staff of support scientists will be happy to assist you in giving Desmond a thorough trial.

Features

Exceptional performance:
Desmond achieves exceptional scalability on commodity Linux clusters with both typical and high-end networks.

Superior accuracy:
Desmond excels in numerical accuracy, which helps to ensure proper modeling of certain thermodynamic relationships that depend on detailed balance. Time-reversible simulations can also be performed. Numerical rigor helps to maintain low energy drift throughout each simulation.

Trusted energetics:
Desmond provides a robust framework for the calculation of energies and forces for various force field models and is compatible with those models commonly used in biomolecular research, including CHARMM, AMBER, and OPLS.

Realistic simulations:
Desmond performs explicit solvent simulations with periodic boundary conditions using cubic, orthorhombic, truncated octahedron, rhombic dodecahedron, and arbitrary triclinic simulation boxes, and can be used to model explicit membrane systems under various conditions.

Quantitative predictions: Desmond computes both absolute and relative solvation free energies as well as relative free energies of binding.

Easy-to-use interface:
Desmond supports automated simulation setup, including highly complex Free Energy Perturbation (FEP) calculations. An intuitive interface provides intelligent default settings and allows for rapid setup of computational experiments. Powerful analysis tools make it possible to visualize and examine computed results within the same Maestro modeling environment.