分子动力学软件选择

分子动力学软件选择

There are widely used packages like AMBER, CHARMm and X-PLOR

https://www.360docs.net/doc/1d4277143.html,/amber/amber.html

https://www.360docs.net/doc/1d4277143.html,/

https://www.360docs.net/doc/1d4277143.html,/

CHARMm and X-PLOR both use the same forcefield. Amber's is different.

If you're Wintel-bound, you could try Hyperchem, which has a free downloadable demo: https://www.360docs.net/doc/1d4277143.html,/products/hc5_features.html

It has a nice structure build capability (the other packages have

powerful languages, but can be intimidating to new users).

OpenSource adherents can find a wealth of free packages at SAL, an

excellent site:

https://www.360docs.net/doc/1d4277143.html,/Z/2/index.shtml

My personal favourites are MMTK, EGO and VMD/NAMD.

I compiled a list of free and commerical programs at

https://www.360docs.net/doc/1d4277143.html,/chemistry/soft_mod_en.html

modeling in solution is possible e.g. with these programs (to the best of my knowledge):

commercial: AMSOL, GROMOS, Titan

free: GAMESOL, GROMACS, MOIL, OMNISOL, Tinker

You find links to all of these programs at

https://www.360docs.net/doc/1d4277143.html,/chemistry/soft_mod_en.html

PAPA (计算粒状物料的三维并行分子动力学计算程序)

【URL】http://www.ica1.uni-stuttgart.de/Research/Software_P3T/papa.html

【作者】 ICA 1 Group, Institute of Computer Applications (ICA) of the University of Stuttgart

【语言版本】 English

【收费情况】免费

【用途】 Characteristic:

dissipative interaction for rotating, rough, spherical particles

geometry elements: walls, cylinders, spheres, etc freely configurable

material properties of walls and particles freely configurable for an arbitray number of materials

object oriented, written in C++

full checkpointing supported

several compilation options: support of X11 graphics, reduction to 2D, debugging aids, etc. Applications:

simulation of granular media, silo filling and steady flow problems, sphere packings of mono- and polydisperse system

ProtoMol (分子动力学并行计算软件)

【URL】https://www.360docs.net/doc/1d4277143.html,/~lcls/Protomol.html

【作者】 LCLS Group at the University of Notre Dame

【语言版本】 English

【操作系统】 SunOS 5.8, IRIX 6.5, Linux 2.4, AIX 5.1

【收费情况】免费

【用途】 PROTOMOL is an object-oriented component based framework for molecular dynamics simulations. The framework supports the CHARMM 19 and 28a2 force fields and is able to process PDB, PSF, XYZ and DCD trajectory files. It is designed for high flexibility, easy extendibility and maintenance, and high performance demands, including parallelization. The technique of multiple time-stepping has been used to improve

long-term efficiency, and the use of fast electrostatic force evaluation algorithms like plain Ewald, Particle Mesh Ewald, and Multigrid summation further improves performance. Longer time steps are possible using MOLLY, Langevin Molly and Hybrid Monte Carlo, Nose-Hoover, and Langevin integrators. In addition, PROTOMOL has been designed to interact with VMD, a visualization engine developed by the University of Illinois that is used for displaying large biomolecular systems in three dimensions. PROTOMOL is free distributed software, and the source code is in cluded.

【相关链接】

VMD (分子可视化软件)

美国圣母大学：计算生命科学实验室

Claessen站点的分子模型化软件

【URL】https://www.360docs.net/doc/1d4277143.html,/chemistry/soft_mod_en.html

【简介】

Molecular Modeling

Commercial Software

3D Viewer: converts 2D structures into 3D with simple MM2

Alchemy 2000: semi empirical, QSAR, Protein, Polymer, LogP

AMPAC: semiempirical quantum mechanical program

AMSOL: semi empirical, solvation models for free energies of solvation in aqueous solutions and in alkane solvents

Personal CAChe: visualize molecules in 3D, search for conformations, analyze chemical reactivity and predict properties of compounds

Quantum CAChe: Personal CaChe plus molecular dynamics and semi-empirical MOPAC and ZINDO quantum mechanics

Chem3D: MOPAC and Gaussian integration, ChemProp, ...

Gaussian 98W: MP2, MP3, MP4, MP5, HF, CASSCF, GVB, QCISD, BD, CCSD, G1, G2, ZINDO, ONIOM calculations, DFT excited states, VCD intensities, ...

GROMOS: general-purpose molecular dynamics computer simulation package for the study of biomolecular systems

Hyperchem Suite: semi empirical, RMS Fit, Molecule Presentations, Sequence Editor, Crystal Builder, Sugar Builder, Conformational Search, QSAR Properties, Script

Editor ...(Hyperchem Pro, Hyperchem Std.)

Jaguar: electronic structure calculation

MacroModel: allows the graphical construction of complex chemical structures mechanics and dynamics techniques in vacuo or in solution

MOPAC 2000: the latest version of MOPAC

Spartan: MM, semiempirical, ab initio, DFT, ...

Titan: TITAN is the union of Wavefunction's versatile, easy-to-use interface with fast, computational algorithms from Schr鰀inger's Jaguar

WinMOPAC: based on MOPAC

Shareware/Freeware

3D Viewer for ISIS Draw: converts 2D structures into 3D with simple MM2

Biomer: online java applet, model builders for polynucleotides (DNA/RNA), polysaccharides and proteins, interactive molecule editor, AMBER force-field based geometry optimization, simulated annealing with molecular dynamics, and the ability to save gif, jpeg, and ppm images

Chem3D Net: demo version of Chem3D

COLUMBUS: high-level ab initio molecular electronic structure calculations

Dalton: quantum chemistry program

GAMESOL: calculate free energies of solvation based on fixed, gas-phase solute geometries interfacing GAMESS

GAMESS: General Atomic and Molecular Electronic Structure System is a general ab initio quantum chemistry package

Gaussian Basis Set: get any Gaussian basis set you can imagine

GROMACS: fully automated topology builder for proteins, molecular dynamics, leap-frog integrator, position langevin dynamics, normal mode analysis, electrostatics,

non-equilibrium MD, NMR refinement with NOE data, large number of powerful analysis tools, ...

Hückel: constructs the Hückel matrix, the programs then calculate, display

MOIL: molecular modeling, energy minimization and molecular dynamics simulation for biomolecules like proteins

Moldy: molecular dynamics simulation program, liquids, solids, rigid surfaces

MOPAC: general purpose semiempirical molecular orbital package for the study of chemical structures and reactions

MOPAC 5.08mn: modified version of MOPAC

NWChem: quantum package for supercomputers and Linux, SCF, RHF, UHF, DFT, CASSCF, interface to Python programming language

OMNISOL: calculating free energies of solvation for organic molecules containing H, C, N, O, F, S, Cl, Br, and I in water and organic solvents

PC GAMESS: GAMESS for the Intel community

Q: molecular dynamics package designed for free energy calculations in biomolecular system

Tinker: molecular modeling software is a complete and general package for molecular mechanics and dynamics

VMD (分子可视化软件)

【URL】https://www.360docs.net/doc/1d4277143.html,/Research/vmd/

【作者】 Biophysics Group,University of Illinois at Urbana-Champaign (UIUC)

【语言版本】 English

【收费情况】免费

【用途】 VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code.

VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. VMD uses OpenGL to provide high performance 3-D molecular graphics

【相关链接】

RasMol:3D分子结构显示程序

PDB文件显示程序KineMage

美国伊利诺依大学：理论生物物理学研究组

JMV (Java分子可视化工具)

ProtoMol (分子动力学并行计算软件)

ORAC (用于模拟溶剂化生物分子的分子动力学计算程序, 意大利佛罗

伦萨大学)

【URL】http://www.chim.unifi.it/orac/

【作者】 Massimo Marchi and P. Procacci

【语言版本】 English

【操作系统】 UNIX

【收费情况】免费

【用途】 ORAC is a program for running classical simulations of biomolecules. Simulations can be carried out in the NVE, NPT, NHP, and NVT thermodynamic ensembles. The integration of the equations of motion in any ensemble can be carried out with the r-RESPA multiple time step integrator and electrostatic interactions can be handled with the Smooth Particle Mesh Ewald method.

【备注】

A parallel version of ORAC4.0 (MPI/T3E) is available upon request to:

Massimo Marchi

Section de Biophysique des Proteines et des Membranes,

DBCM, DSV, CEA, Centre d'Etudes,

Saclay, 91191 Gif-sur-Yvette Cedex, FRANCE

Virtual Molecular Dynamics Laboratory (分子动力学软件)

【URL】https://www.360docs.net/doc/1d4277143.html,/vmdl/index.html

【作者】 Amit Bansil, Lidia Braunstein

【语言版本】 English

【收费情况】免费

【用途】 The Virtual Molecular Dynamics Laboratory enables the student to visualize atomic motion, manipulate atomic interactions, and quantitatively investigate the resulting macroscopic properties of biological, chemical, and physical systems.

The Virtual Laboratory is a suite of research-based molecular dynamics software tools

and project-based curriculum guides. The software tools are: "Simple Molecular Dynamics (SMD)", "Universal Molecular Dynamics", and "Water".

【相关链接】

美国波士顿大学聚合物研究中心(可视化模拟)

DL_POLY (分子动力学模拟软件)

【URL】https://www.360docs.net/doc/1d4277143.html,/msi/software/DL_POLY/

【作者】 W. Smith and T.R. Forester

【语言版本】 English

【收费情况】免费

DL_POLY is supplied to individuals under a licence and is free of cost to academic scientists pursuing scientific research of a non-commercial nature. A group licence is also available for academic research groups. All recipients of the code must first agree to the terms of the licence.

Commercial organisations interested in acquiring the package should approach Dr. W. Smith at Daresbury Laboratory in the first instance. Daresbury Laboratory is the sole centre for distribution of the package.

【用途】 DL_POLY is a general purpose serial and parallel molecular dynamics simulation package originally developed at Daresbury Laboratory by W. Smith and T.R. Forester under the auspices of the Engineering and Physical Sciences Research Council (EPSRC) for the EPSRC's Collaborative Computational Project for the Computer Simulation of Condensed Phases (CCP5) and the Molecular Simulation Group (MSG) at Daresbury Laboratory. The package is the property of the Central Laboratory of the Research Councils.

Two versions of DL_POLY are currently available. DL_POLY_2 is the original version which has been parallelised using the Replicated Data strategy and is useful for simulations of up to 30,000 atoms on 100 processors. DL_POLY_3 is a version which uses Domain Decomposition to achieve parallelism and is suitable for simulations of order 1 million atoms on 8-1024 processors.

DL_POLY (分子动力学模拟软件)

【URL】https://www.360docs.net/doc/1d4277143.html,/msi/software/DL_POLY/

【作者】 W. Smith and T.R. Forester

【语言版本】 English

【收费情况】免费

DL_POLY is supplied to individuals under a licence and is free of cost to academic

scientists pursuing scientific research of a non-commercial nature. A group licence is also available for academic research groups. All recipients of the code must first agree to the terms of the licence.

Commercial organisations interested in acquiring the package should approach Dr. W. Smith at Daresbury Laboratory in the first instance. Daresbury Laboratory is the sole centre for distribution of the package.

【用途】 DL_POLY is a general purpose serial and parallel molecular dynamics simulation package originally developed at Daresbury Laboratory by W. Smith and T.R. Forester under the auspices of the Engineering and Physical Sciences Research Council (EPSRC) for the EPSRC's Collaborative Computational Project for the Computer Simulation of Condensed Phases (CCP5) and the Molecular Simulation Group (MSG) at Daresbury Laboratory. The package is the property of the Central Laboratory of the Research Councils.

Two versions of DL_POLY are currently available. DL_POLY_2 is the original version which has been parallelised using the Replicated Data strategy and is useful for simulations of up to 30,000 atoms on 100 processors. DL_POLY_3 is a version which uses Domain Decomposition to achieve parallelism and is suitable for simulations of order 1 million atoms on 8-1024 processors.

PMDS (并行分子动力学模板库)

【URL】http://stencil.koma.jaeri.go.jp/

【作者】 Japan Atomic Energy Research Institute

【语言版本】 English

【收费情况】免费

【用途】 Parallel Molecular Dynamics Stencil (PMDS) is an assembly of subroutine programs for executing parallel short-range molecular-dynamics simulations of solids. PMDS is written in C language using MPI for parallelization, and is designed to separate and conceal parts of the programs for parallel algorithms such as inter-processor communications so that parallel programming for force calculation can be done in the same way as serial programming; it can be easily revised according to physical models.

MDRANGE (分子动力学计算ion ranges)

【URL】http://beam.helsinki.fi/~knordlun/mdh/mdh_program.html

【作者】 Kai Nordlund

【语言版本】 English

【收费情况】免费

【用途】 The official name of the program is MDRANGE. However, in the actual program files the shorter, more convenient name mdh (abbreviated from Molecular Dynamics High-energy) is used. Both names therefore (at least for now) mean exactly the same program. The program is a molecular dynamics (MD) simulation program tailored for effective calculation of ion ranges. The word effective used here must be understood in the context of high-energy molecular dynamics calculations.

What it does

Calculates ion ranges in solids

Calculates deposited energies

Calculates the primary recoil spectrum

Obtaining stopping powers possible indirectly

Ion and sample elements which can be used: any

Energy range in which calculation can be done: roughly 1 eV/amu - 10 MeV/amu

Energy range in which use is justified: roughly 100 eV/amu - 100 keV/amu

MDRANGE3.0: option for Puska-Echenique-Nieminen-Ritchie(PENR)-electronic stopping model [Sil00]. Needs charge density file from user.

MDRANGE3.0: option for Brandt-Kitakawa(BK)-electronic stopping model. Needs charge density file from user.

【备注】

Kai Nordlund

Accelerator Laboratory, University of Helsinki, P.O. BOX 43, FIN-00014 Helsinki, Finland (email kai.nordlund@helsinki.fi)

Car-Parrinello分子动力学(CPMD, ab-initio分子动力学计算软件)

【URL】https://www.360docs.net/doc/1d4277143.html,/

【作者】 Jurg Hutter

【语言版本】 English

【操作系统】 Unix/Linux

【下载】 https://www.360docs.net/doc/1d4277143.html,/ftp.html

【收费情况】免费

【用途】泛函：LDA，LSD，GGA，自由能密度泛函。

孤立体系和周期边界体系的计算。

对分子和晶体使用对称性。

波函优化。

几何优化与过渡态寻找。

恒定能量，恒温，恒压的分子动力学。

路径积分分子动力学。

线性响应函数计算，NMR，Raman和IR。

TDDFT计算激发态。

多电子特性。

周期体系的偶极矩。

激发态的分子动力学。

QM/MM方法。

OpenMP并行化。

【备注】

Its first version was developed by Jurg Hutter at IBM Zurich

Research Laboratory starting from the original Car-Parrinello codes. During the years many people from diverse

organizations contributed to the development of the code and of its pseudopotential library: Michele Parrinello, Jurg Hutter, D. Marx, P. Focher, M. Tuckerman, W. Andreoni, A. Curioni, E. Fois, U. Roetlisberger, P. Giannozzi, T. Deutsch, A. Alavi, D. Sebastiani, A. Laio, J. VandeVondele, A. Seitsonen, S. Billeter and others.

GROMACS (分子动力学软件)

【URL】https://www.360docs.net/doc/1d4277143.html,

【作者】 Dep. of Biophysical Chemistry, Groningen University

【语言版本】 C

【操作系统】 Unix

【下载】 https://www.360docs.net/doc/1d4277143.html,/download/index.php

【收费情况】免费

免费

【用途】 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 and lipids 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.

GROMACS supports all the usual algorithms you expect from a modern molecular dynamics implementation, but there are also quite a few features that make it stand out from the competition:

* GROMACS provides extremely high performance compared to all other programs.

* GROMACS is user-friendly, with topologies and parameter files written in clear text format.

* There is no scripting language - all programs use a simple interface with command line options for input and output files.

* As the simulation is proceeding, GROMACS will continuously tell you how far it has

come, and what time and date it expects to be finished.

* Both run input files and trajectories are independent of hardware endian and can thus be read by any version GROMACS, even if it was compiled using a different floating-point precision. All files from GROMACS 2.0 can further be used in the new version 3!

* GROMACS can write coordinates using lossy compression, which provides a very compact way of storing trajectory data. The accuracy can be selected by the user.

* GROMACS comes with a large selection of flexible tools for trajectory analysis - you won't have to write any code to perform routine analyses. The output is further provided in the form of finished Xmgr/Grace graphs, with axis labels, legends, etc. already in place!

* A basic trajectory viewer that only requires standard X libraries is included, and several external visualization tools can read the GROMACS file formats.

* GROMACS can be run in parallel, using standard MPI communication.

* GROMACS contains several state-of-the-art algorithms that make it possible to extend the time steps is simulations significantly, and thereby further enhance performance without sacrificing accuracy or detail.

* The package includes a fully automated topology builder for proteins, even multimeric structures. Building blocks are available for the 20 standard aminoacid residues as well as some modified ones, the 4 nucleotide and 4 deoxinucleotide resides, several sugars and lipids, and some special groups like hemes and several small molecules.

* There is ongoing development to extend GROMACS with interfaces both to Quantum Chemistry and Bioinformatics/databases.

【使用说明链接】 https://www.360docs.net/doc/1d4277143.html,/documentation/index.php

美国能源部Ames实验室：经典分子动力学软件AL_CMD

【URL】https://www.360docs.net/doc/1d4277143.html,/cmp/CMP_Theory/cmd/alcmd_source.html

【作者】 Dave Turner, Jamie Morris

【语言版本】 English

【系统配置要求】 Intel Paragon, nCube 2S, IBM SP-2, scalar computers

【收费情况】免费

【用途】 This code is provided to the general public by Ames Laboratory, as part of the HPCC Materials Science Grand Challenge project of the U.S. Department of Energy. A spatial decomposition approach enables it to run efficiently on a wide variety of computers including the Intel Paragon, nCube 2S, IBM SP-2, scalar computers, or any parallel computer that utilizes the MPI communications library. A variety of classical atomic

interactions are supported including simple Leonard-Jones pair interactions, the Embedded-Atom Method, and 3-body interactions using Tersoff potentials.

【备注】

All researchers utilizing this code should acknowledge Ames Laboratory and the U.S. Department of Energy in any published work, and email them a citation on where it was published.

turner@https://www.360docs.net/doc/1d4277143.html,

or

jrmorris@https://www.360docs.net/doc/1d4277143.html,.

MDynaMix (分子动力学计算软件)

【URL】http://www.fos.su.se/physical/sasha/md_prog.html

【作者】 Alexander Lyubartsev

【语言版本】 English

【操作系统】 PC-Pentium (PPro,PII) Linux 2.0 and more

【收费情况】免费

【用途】 This is a general purpose molecular dynamics code for simulations of mixtures of either rigid or flexible molecules, interacting by AMBER-like force field in a periodic rectangular cell. In the case of flexible molecules the double time step algorithm is used. Algorithms for NVE, NVT and NPT statistical ensembles are employed, as well as optimized Ewald sum for treatment of the electrostatic interactions. The program can be run both in sequential and parallel execution. The parallel version employes "replicated data" strategy. It can be run on any parallel architecture or workstation cluster with MPI parallel environment installed.

This program was originally based on the MOLDYN program by Aatto Laaksonen available from the CCP5 program library , Daresbury Lab, UK. Since 1993 many additional changes were made by Alexander Lyubartsev, some of these are:

NVT ensemble (v2.1)

NPT ensemble (v3.0)

complex DNA-like molecules (v3.5)

non-cubic (rectangular) cell, optimized Evald sum calculation (v3.6)

hydrogen bonds included (10-12 potential) (v3.7)

first parallel version (v3.8)

fully parallelized code (v4.0)

several types of dihedral angles potentials, Morse bond potential (v.4.1) New (free) format of input data.

option for separate pressure controll in each direction; reaction field method method for the electrostatic interactions; options for truncated octahedron or hexagonal simulation cell (v4.2)

explicit reversible integrator for NPT-dynamics (Martyna et all, J.Chem.Phys, 101, 4177 (1994) is implemented; option for ASCII format of the restart file; some other options; more comments in the source files (v.4.3); utility "makemol" for easier constructing of molecular models is added

【相关链接】

瑞典斯德哥尔摩大学：阿列纽斯实验室物理化学研究组

Molecular Dynamics on Parallel Computers (并行计算机上的分子动力

学)

【URL】https://www.360docs.net/doc/1d4277143.html,.sg/books/physics/4353.html

【作者】Rüdiger Esser, Peter Grassberger, Johannes Grotendorst, Marius Lewerenz 【出版者】World Scientific

【出版日期】Feb 2000

【价格】US$93 / ￡63

【ISBN】981-02-4232-8

【主要内容】

Molecular dynamics is a well-established technique for simulating complex

many-particle systems in many areas of physics, chemistry, and astrophysics. The huge computational requirements for simulations of large systems, especially with long-range forces, demand the use of massively parallel computers. Designing efficient algorithms for these problems is a highly non-trivial task.

This book contains the invited talks and abstracts presented at a conference by more than 100 researchers from various fields: computer science, solid state physics, high energy physics, polymers, biochemistry, granular materials and astrophysics. Most of the contributions have been written by users of massively parallel computers and deal with practical issues, but there are also contributions tackling more fundamental algorithmic problems.

GROMOS (通用分子动力学软件包)

【URL】http://www.igc.ethz.ch/gromos/

【作者】 Laboratory of Physical Chemistry,ETH

【语言版本】 English

【收费情况】部分免费

free for academics

This means that GROMOS96 is available for non-commercial institutes at the price of US $ 400,- which is meant to cover costs of administration (manual, correction letters, etc.) and distribution medium handling. For this amount, help with installation of GROMOS or

familiarization with it cannot be expected. Industry has to pay substantially more for GROMOS (US $ 12000.-, additional information)

【用途】 GROMOS is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems. Its purpose is threefold:

a. Simulation of arbitrary molecules in solution or crystalline state by the method of molecular dynamics (MD), stochastic dynamics (SD) or the path-integral method.

b. Energy minimisation of arbitrary molecules.

c. Analysis of conformations obtained by experiment or by computer

simulation.

The simulation package comes with the GROMOS force field (proteins, nucleotides, sugars, etc.) the quality of which should be judged from the scientific literature concerning its application to chemical and physical systems, ranging from glasses and liquid crystals to polymers and crystals and solutions of biomolecules.

【备注】

free for academics

模拟蛋白质的并行分子动力学计算程序EGO

【URL】http://www.lrz-muenchen.de/~heller/ego/

【作者】 Markus Eichinger, Helmut Heller and Helmut Grubmueller

【语言版本】 English

【收费情况】免费

【用途】 EGO is a program to perform molecular dynamics simulations on parallel as well as on sequential computers. Supported parallel machines include the Hitachi SR8000, CRAY-T3E, IBM-SP2, Fujitsu VPP700, Parsytec-CC under PARIX and inhomogeneous clusters of UNIX workstations under PVM or MPI. EGO also runs sequentially on any decent UNIX workstation; even Windows95/NT PC's (with a GNU-C compiler) can be used.

EGO was developed for the simulation of large molecular systems on parallel computers (under PVM, MPI or PARIX). EGO uses a multiple time step algorithm combined with a structure adapted fast multipole method for the description of long range electrostatics. The method has been demonstrated to scale linearly with the number of atoms in the range of about 40,000 atoms.

NAMD (并行分子动力学计算软件)

【URL】https://www.360docs.net/doc/1d4277143.html,/Research/namd/

【作者】 Theoretical and Computational Biophysics Group,University of Illinois at Urbana-Champaign (UIUC)

【语言版本】 English

【收费情况】免费

【用途】 NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using switched fast ethernet. NAMD is file-compatible with AMBER, CHARMM, and

X-PLOR and is distributed free of charge with source code.

Current NAMD Feature Summary:

Software Setup

Free to download and use. (Redistribution prohibited.)

Precompiled binaries provided for 12 popular platforms.

Installed at major NSF supercomputer sites.

Portable to virtually any platform with ethernet or MPI.

C++ source code and CVS access for modification.

Molecule Building

Reads X-PLOR, CHARMM, AMBER, and GROMACS input files.

Psfgen tool generates structure and coordinate files for CHARMM force field.

Efficient conjugate gradient minimization.

Fixed atoms and harmonic restraints.

Thermal equilibration via periodic rescaling, reinitialization, or Langevin dynamics.

Basic Simulation

Constant temperature via rescaling, coupling, or Langevin dynamics.

Constant pressure via Berendsen or Langevin Nose-Hoover methods.

Particle mesh Ewald full electrostatics for periodic systems.

Symplectic multiple timestep integration.

Rigid waters and bonds to hydrogen atoms.

Advanced Simulation

Chemical and conformational free energy calculations.

Locally enhanced sampling via multiple images.

Tcl based scripting and steering forces.

Interactive visual steering interface to VMD.

Scalable Performance

Based on the Charm++/Converse parallel runtime system.

Spatial data decomposition for limited communication pattern.

Message driven execution for latency tolerance on commodity networks.

Measurement-based load balancing for scaling to hundreds of processors.

Largest simulation to date is over 300,000 atoms on 1000 processors.

【相关链接】

美国伊利诺依大学：理论生物物理学研究组

DPMTA (分子动力学并行模拟软件)

【URL】https://www.360docs.net/doc/1d4277143.html,/~wrankin/Dpmta/index.html

【作者】 William T. Rankin

【语言版本】 English

【收费情况】免费

【用途】 DPMTA is targeted mainly for the high precision requirements of Molecular Dynamics (MD) simulations, its generic interface makes it useful for many other applications. DDPMTA is a portable implementation of the Paralel Multipole Tree Algorithm (PMTA) which runs in a distributed environment under the both PVM and MPI toolset.DPMTA provides application programmers with an easy to use interface to compute full N-body interaction solutions.

Main Features:

Implements an efficient heirarchical multiple algorithm.

Uses efficient F and G Multipole Formulation for added performance.

User selectable processing paramenters allows application specific tradeoff between accuracy, problem size and execution time. DPMTA allows the user to set exact upper error boundaries.

A simple application interface that allows quck and easy integration of DPMTA into existing application programs.

Portable to wide vairiety of Unix and other platforms. DPMTA will run on any number of processors with excellent scalability (>75% on many platforms).

Can compute multipole-based Lennard-Jones Interactions.

Handles parallel-piped non-cubic simulation regions.

Performs Macroscopic Assembly Compuations as an alternative to Ewald summation to simulation infinite periodic latices. In addition, DPMTA can perform simple periodic boundary computations.

Runs as a distributed parallel process under PVM, MPI, or as an efficient serial algorithm. Computes Virial Tensor approximations for constant pressure simulations.

Allows programmer to use Morton, Hilbert, or Row/Column ordering of cells for efficient distributed allocation of work among processors.

Implements a simple Load Balancing algorithm to efficiently partition the computation distribution when used in a distributed environment.

【相关链接】

美国杜克大学：化学系

SIGMA (分子动力学相关软件)

【URL】https://www.360docs.net/doc/1d4277143.html,/SIGMA/

【作者】 Jan Hermans, R. H. Yun, Jon Leech, David Cavanaugh, Hao Hu

【语言版本】 English

【用途】 SIGMA is a system of programs and data files for doing Energy minimization, Free Molecular dynamics, Constrained and restrained molecular dynamics, and Molecular dynamics with free-energy methods of biological macromolecules. Using Sigma one can work with periodic boundary conditions and simulate molecules in solvent water.

【备注】

Department of Biochemistry and Biophysics

University of North Carolina

Chapel Hill, N.C. 27599-7260

(919) 966-4644

hermans@https://www.360docs.net/doc/1d4277143.html,

并行分子动力学模拟软件DoD-TBMD

【URL】https://www.360docs.net/doc/1d4277143.html,/~mehl/tbmd/

【作者】 Florian Kirchhoff

【语言版本】 English

【收费情况】免费

【用途】 DoD-TBMD is a code for doing molecular dynamics simulations of metallic systems. It uses a quantum-mechanical description of the inter-atomic interactions. The Hamiltonian of the system is approximated using an empirical tight-binding model. The electronic-structure is calculated either by direct diagonalization or by using an O(N2) method called the Kernel Polynomial Method (KPM). The code has been written for both scalar and parallel computers. The parallel parts of the code have been written using a message-passing programming model relying on the MPI library to deal with communications.

【备注】

If you have any comments, suggestions or questions

send Florian Kirchhoff an e-mail at kirchhoff.5@https://www.360docs.net/doc/1d4277143.html, (Privacy Advisory) MOLECULAR-DYNAMICS-NEWS List (分子动力学与化学物理学)

【URL】https://www.360docs.net/doc/1d4277143.html,/lists/molecular-dynamics-news.html 【介绍】

News for the molecular dynamics and chemical physics community. 【查询过去的Postings】

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