Tag: Dynamics Simulation

Desmond 2023.2 – High-speed Molecular Dynamics Simulation

Desmond 2023.2

:: 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.

::DEVELOPER

D. E. Shaw Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Window / Linux / Mac OsX
  • Python

:: DOWNLOAD

Desmond

:: MORE INFORMATION

Citation

Kevin J. Bowers, Edmond Chow, Huafeng Xu, Ron O. Dror, Michael P. Eastwood, Brent A. Gregersen, John L. Klepeis, István Kolossváry, Mark A. Moraes, Federico D. Sacerdoti, John K. Salmon, Yibing Shan, and David E. Shaw,
“Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters,”
Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), Tampa, Florida, November 11–17, 2006

AmberTools 20 – Molecular Dynamics Simulation

AmberTools 20

:: DESCRIPTION

AmberTools consists of several independently developed packages that work well by themselves, and with Amber (Assisted Model Building with Energy Refinement) itself. The suite can also be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB), with generalized Born solvent models.

AmberTools consists of 7 main codes
NAB build molecules; run MD or distance geometry, using generalized Born, Poisson-Boltzmann or 3D-RISM implicit solvent models
antechamber Create force fields for general organic molecules
ptraj Analyze trajectories from Amber or CHARMM
tleap and xleap Basic preparation program for Amber simulations
sleap replaces and expands tleap
sqm semiempirical and DFTB quantum chemistry program
pbsa Performs numerical solutions to Poisson-Boltzmann models

::DEVELOPER

AMBER Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  MacOsX / Window with Cygwin

:: DOWNLOAD

AmberTools

:: MORE INFORMATION

Citation

D.A. Case, T.E. Cheatham, III, T. Darden, H. Gohlke, R. Luo, K.M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods.
The Amber biomolecular simulation programs.
J. Computat. Chem. 26, 1668-1688 (2005).