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

/amber/

/

/

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: /products/hc5_

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:

/Z/2/

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

I compiled a list of free and commerical programs at

/chemistry/soft_mod_

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

/chemistry/soft_mod_

PAPA (

计算粒状物料的三维并行分子动力学计算程序

)

【

URL

】

/Research/Software_P3T/

【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

】

/~lcls/

【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

】

/chemistry/soft_mod_

【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, ...

Hü

ckel: constructs the Hü

ckel 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

】

/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

】

/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

】

/vmdl/

【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:

(SMD)

【相关链接】

美国波士顿大学聚合物研究中心

(< /p>

可视化模拟

)

DL_POLY (

分子动力学模拟软件

)

【

URL

】

/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

】

/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

】

/

【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

】

/~knordlun/mdh/mdh_

【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 nd@)

Car- Parrinello

分子动力学

(CPMD, ab- initio

分子动力学计算软件

)

【

URL

】

/

【作者】

Jurg Hutter

【语言版本】

English

【操作系统】

Unix/Linux

【下载】

/

【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