Softwares for Molecular Dynamics

 

Classical MD

1. LAMMPS
   LAMMPS is a classical molecular dynamics code with a focus on materials modeling. It’s an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

   LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

   LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. Many of its models have versions that provide accelerated performance on CPUs, GPUs, and Intel Xeon Phis. The code is designed to be easy to modify or extend with new functionality.

   LAMMPS is distributed as an open source code under the terms of the GPL. The current version can be downloaded here. Links are also included to older versions. All LAMMPS development is done via GitHub, so all versions can also be accessed there. Periodic releases are also posted to SourceForge.

   LAMMPS is distributed by Sandia National Laboratories, a US Department of Energy laboratory. The main authors of LAMMPS are listed on this page along with contact info and other contributors. Funding for LAMMPS development has come primarily from DOE (OASCR, OBER, ASCI, LDRD, Genomes-to-Life) and is acknowledged here.

   The LAMMPS web site is hosted by Sandia, which has this Privacy and Security statement.

   · Platform: Unix-like, Windows
   · Host: Sandia National Laboratory, USA. （桑迪亚国家实验室 · 美国）

2. IMD
   IMD, i.e. The ITAP Molecular Dynamics Program, is a software package for classical molecular dynamics simulations. Several types of interactions are supported, such as central pair potentials, EAM potentials for metals, Stillinger-Weber and Tersoff potentials for covalent systems, and Gay-Berne potentials for liquid crystals. A rich choice of simulation options is available: different integrators for the simulation of the various thermodynamic ensembles, options that allow to shear and deform the sample during the simulation, and many more. There is no restriction on the number of particle types.

   The main design goals were to create a flexible and modular software reaching high performance on contemporary computer architectures, while being as portable as reasonably possible. IMD runs efficiently on both single processor workstations and massively parallel supercomputers, but is not very well suited for vector processors. The parallelization uses the standard MPI library for message passing. As IMD is written in ANSI C, it should be easily portable to any Unix-like environment.

   IMD even received a prize, and holds a world record.

   The development of IMD is supported by the SFB 716.

   Platform: Unix-like
   Host: Universität Stuttgart, Germany. （斯图加特大学 · 德国）

Long Timescale MD

1. EON
   The EON software package contains a set of algorithms used primarily to model the evolution of atomic scale systems over long time scales. Standard molecular dynamics algorithms, based upon solving Newton’s equations, are limited by the femtosecond time scale of atomic vibrations. EON simulations are designed for rare event systems where the interesting dynamics can be described by fast transition between stable states. In each algorithm, the residence time in the stable states is modeled with statistical mechanics, and the important state-to-state dynamics are modeled stochastically.

   The algorithms currently implemented include parallel replica dynamics, hyperdyamics, adaptive kinetic Monte Carlo, and basin hopping.

基于第一性原理的分子动力学模拟

QUANTUM ESPRESSO

This is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

ABINIT

ABINIT is a software suite to calculate the optical, mechanical, vibrational, and other observable properties of materials. Starting from the quantum equations of density functional theory, you can build up to advanced applications with perturbation theories based on DFT, and many-body Green’s functions (GW and DMFT) .

ABINIT can calculate molecules, nanostructures and solids with any chemical composition, and comes with several complete and robust tables of atomic potentials.

On-line tutorials are available for the main features of the code, and several schools and workshops are organized each year.

这个软件在另一个机构也有被提到，European Theoretical Spectroscopy Facility, 并提供指导.

CPMD

The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.

The General Atomic and Molecular Electronic Structure System

This is a general ab initio quantum chemistry package, and maintained by the members of the Gordon research group at Iowa State University.

VASP

大名鼎鼎的vasp了

Other MD simulators

1. CHARMM
   focus on proteins and nucleic acids

Comparison of software for molecular mechanics modeling

当前分子动力学模拟软件对比