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Matlab

Gromacs

Namd

Gandi

Amber

Autodock

Lammps

AMBER

DL_POLY is a molecular dynamics package developed at the STFC Daresbury Laboratory for UK computational chemists, which uses Domain Decomposition to achieve parallelism and is suitable for simulations of the order 1 million atoms which run on more than 8 processors. For more information please refer to: original document  

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AutoDock

AutoDock  is  an  automated  procedure  for  predicting  the  interaction  of  ligands  with biomacromolecular  targets. It is a suite of automated docking tools, designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AutoDock 4 actually consists of two main programs: autodock performs the docking of …

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GANDI

GANDI assembles molecules by joining fragments, which have been previously docked into a protein binding site (henceforth referred to as receptor), with user-defined linker fragments. Heavy atom – hydrogen atom vectors constitute the possible attachment points on both the docked fragments and the linkers. The build-up method implemented in GANDI uses a combination of a …

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GROMACS

GROMACS is a versatile package to perform molecular dynamics and energy minimization, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.  It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at …

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LAMMPS

LAMMPS is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, metallic, granular, and coarse−grained systems using a variety of force fields and boundary conditions. LAMMPS can model systems with only a few particles up to millions or billions. LAMMPS …

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MATLAB

MATLAB (Matrix laboratory) is a high-performance language for scientific computing. It integrates computation, visualization, simulation and programming environments. These factors make MATLAB an excellent tool for research objectives.   The Parallel Computing Toolbox (PCT) is a MATLAB toolbox solving computation-intensive and data-intensive problems using MATLAB more quickly — on local multicore computer, Cluster of computers …

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NAMD

NAMD (Not (just) Another Molecular Dynamics program) is a free-of-charge parallel molecular dynamics simulation package written using the Charm++ parallel programming model. Namd is noted for its parallel efficiency and often used to simulate large systems (millions of atoms). It scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity …

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