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AMBER

Amber is a suite of biomolecular simulation programs. It began in the late 1970's, and is maintained by an active development community; see our history page and our contributors page for more information.

The term "Amber" refers to two things. First, it is a set of molecular mechanical force fields for the simulation of biomolecules (these force fields are in the public domain, and are used in a variety of simulation programs). Second, it is a package of molecular simulation programs which includes source code and demos.

DHFR NPT HMR 4fs = 23,558 atoms

Typical Production MD NPT, MC Bar 4fs HMR

  &cntrl

    ntx=5, irest=1,

    ntc=2, ntf=2,

    nstlim=75000,

    ntpr=1000, ntwx=1000,

    ntwr=10000,

    dt=0.004, cut=8.,

    ntt=1, tautp=10.0,

    temp0=300.0,

    ntb=2, ntp=1, barostat=2,

    ioutfm=1,

     &end

    Single job throughput

    (a single run on one or more GPUs within a single node)

GROMACS

GROMACS is a versatile package to perform molecular dynamics, 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 calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

The work that went into the GPU acceleration actually also improved CPU performance significantly when comparing release 4.6 with release 4.5. Here's an example of a membrane protein, the ligand-gated ion channel GLIC embedded in a lipid bilayer and surrounded by water and ions, totaling about 150,000 atoms. This system uses 2fs time steps, and got almost 40% better performance in Gromacs-4.6, even when staying completely on the CPU. Nevertheless, the new GPU performance leaves this far behind - it is roughty five-fold faster than Gromacs-4.5。