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 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: 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: My personal favourites are MMTK, EGO and VMD/NAMD. I compiled a list of free and commerical programs at 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 PAPA (计算粒状物料的三维并行分子动力学计算程序) 【URL】  【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/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】  【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】  【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