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/amber.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: /products/hc5_features.htmlIt has a nice structure build capability (the other packages havepowerful languages, but can be intimidating to new users).OpenSource adherents can find a wealth of free packages at SAL, anexcellent site:/Z/2/index.shtmlMy personal favourites are MMTK, EGO and VMD/NAMD.I compiled a list of free and commerical programs at/chemistry/soft_mod_en.htmlmodeling in solution is possible e.g. with these programs (to the best of my knowledge):commercial: AMSOL, GROMOS, Titanfree: GAMESOL, GROMACS, MOIL, OMNISOL, TinkerYou find links to all of these programs at/chemistry/soft_mod_en.htmlPAPA (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 particlesgeometry elements: walls, cylinders, spheres, etc freely configurablematerial properties of walls and particles freely configurable for an arbitray number of materialsobject oriented, written in C++full checkpointing supportedseveral 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 systemProtoMol (分子动力学并行计算软件)【URL】/~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 improvelong-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_en.html【简介】Molecular ModelingCommercial Software3D Viewer: converts 2D structures into 3D with simple MM2Alchemy 2000: semi empirical, QSAR, Protein, Polymer, LogPAMPAC: semiempirical quantum mechanical programAMSOL: semi empirical, solvation models for free energies of solvation in aqueous solutions and in alkane solventsPersonal CAChe: visualize molecules in 3D, search for conformations, analyze chemical reactivity and predict properties of compoundsQuantum CAChe: Personal CaChe plus molecular dynamics and semi-empirical MOPAC and ZINDO quantum mechanicsChem3D: 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 systemsHyperchem Suite: semi empirical, RMS Fit, Molecule Presentations, Sequence Editor, Crystal Builder, Sugar Builder, Conformational Search, QSAR Properties, ScriptEditor ...(Hyperchem Pro, Hyperchem Std.)Jaguar: electronic structure calculationMacroModel: allows the graphical construction of complex chemical structures mechanics and dynamics techniques in vacuo or in solutionMOPAC 2000: the latest version of MOPACSpartan: 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 JaguarWinMOPAC: based on MOPACShareware/Freeware3D Viewer for ISIS Draw: converts 2D structures into 3D with simple MM2Biomer: 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 imagesChem3D Net: demo version of Chem3DCOLUMBUS: high-level ab initio molecular electronic structure calculationsDalton: quantum chemistry programGAMESOL: calculate free energies of solvation based on fixed, gas-phase solute geometries interfacing GAMESSGAMESS: General Atomic and Molecular Electronic Structure System is a general ab initio quantum chemistry packageGaussian Basis Set: get any Gaussian basis set you can imagineGROMACS: 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, displayMOIL: molecular modeling, energy minimization and molecular dynamics simulation for biomolecules like proteinsMoldy: molecular dynamics simulation program, liquids, solids, rigid surfacesMOPAC: general purpose semiempirical molecular orbital package for the study of chemical structures and reactionsMOPAC 5.08mn: modified version of MOPACNWChem: quantum package for supercomputers and Linux, SCF, RHF, UHF, DFT, CASSCF, interface to Python programming languageOMNISOL: calculating free energies of solvation for organic molecules containing H, C, N, O, F, S, Cl, Br, and I in water and organic solventsPC GAMESS: GAMESS for the Intel communityQ: molecular dynamics package designed for free energy calculations in biomolecular systemTinker: molecular modeling software is a complete and general package for molecular mechanics and dynamicsVMD (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】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 MarchiSection de Biophysique des Proteines et des Membranes,DBCM, DSV, CEA, Centre d'Etudes,Saclay, 91191 Gif-sur-Yvette Cedex, FRANCEVirtual Molecular Dynamics Laboratory (分子动力学软件)【URL】/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 toolsand 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】/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 academicscientists 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 doesCalculates ion ranges in solidsCalculates deposited energiesCalculates the primary recoil spectrumObtaining stopping powers possible indirectlyIon and sample elements which can be used: anyEnergy range in which calculation can be done: roughly 1 eV/amu - 10 MeV/amuEnergy range in which use is justified: roughly 100 eV/amu - 100 keV/amuMDRANGE3.0: 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 NordlundAccelerator 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】/【作者】 Jurg Hutter【语言版本】 English【操作系统】 Unix/Linux【下载】 /ftp.html【收费情况】免费【用途】泛函：LDA，LSD，GGA，自由能密度泛函。