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用户:Njzjz/分子力学建模软件比较

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这是主要用于分子力学计算的软件列表。

软件名称 三维显示 构建模型 最优化 分子动力学 蒙地卡罗方法 并行退火 量子力学 隐含的水 GPU（英语：Molecular modeling on GPUs） 注释 软件许可证 网站
Abalone（英语：Abalone (molecular mechanics)） 是 是 是 是 是 是 I 是 是 生物分子模拟、蛋白质折叠 专有, gratis, 商业软件 Agile Molecule
ACEMD[1] 否 否 是 是 否 是 否 否 是 基于CHARMM力场的分子动力学；运行于NVIDIA GPU上，CUDA高度优化 专有、免费和商业版本 Acellera Ltd[永久失效链接]
ADF（英语：Amsterdam Density Functional） 是 是 是 是 否 否 是 是 是 Modeling suite: ReaxFF, UFF, QM-MM with Amber and Tripos force fields, DFT and semi-empirical methods, conformational analysis with RDKit; partly GPU-accelerated 专有, 商业软件, gratis trial SCM
ADUN[2] 否 否 是 是 否 否 是 是 是 Charmm, AMBER, user specified (via force field markup language, FFML), QM-MM calculations with empirical valence bond (EVB); framework based (GNUStep-Cocoa); SCAAS for spherical boundary conditions 免费 open source GNU GPL https://web.archive.org/web/20160303133843/https://gna.org/projects/adun
Assisted Model Building with Energy Refinement (AMBER)[3] 否 是 是 是 否 是 I 是 是 ? 专有 ambermd.org
Ascalaph Designer 是 是 是 是 是 是 I 是 是 Molecular building (DNA, proteins, hydrocarbons, nanotubes), molecular dynamics, GPU acceleration Mixed: free open source (GNU GPL) & 商业软件 Ascalaph Project
Automated Topology Builder (ATB) 是 是 是 否 否 否 否 否 否 Automated molecular topology building service for small molecules (< 99 atoms). GROMOS, GROMACS, CNS, LAMMPS formats with validation
Repository for molecular topologies and pre-equilibrated systems 		专有 商业软件, gratis academic use Automated Topology Builder
Avogadro 是 是 是 否 否 否 I 否 否 Molecule building, editing (peptides, small molecules, crystals), conformational analysis, 2D/3D conversion; extensible interfaces to other tools 免费 open source GNU GPL Avogadro
BOSS 否 否 是 否 是 否 是 否 否 OPLS 专有 Yale University
CHARMM 否 是 是 是 是 I I 是 是 Commercial version with multiple graphical front ends is sold by Accelrys (as CHARMm) 专有, 商业软件 charmm.org
ChemDoodle 3D 是 是 是 否 否 否 否 否 否 Intuitive building of molecules in real-time; production of high quality publication graphics; works on Windows, macOS and Linux; developed by iChemLabs 专有, 商业软件, free trial ChemDoodle 3D Website
CHEMKIN 否 否 否 否 否 否 否 否 否 Chemical reaction kinetics. 专有 CHEMKIN
COSMOS 是 是 是 是 是 否 I 否 否 Hybrid QM-MM COSMOS-NMR force field with fast semi-empirical calculation of electrostatic and/or NMR properties; 3-D graphical molecule builder and viewer 专有, 商业软件, free without GUI COSMOS Software
CP2K 否 否 是 是 是 否 是 是 是 CP2K can perform atomistic and molecular simulations of solid state, liquid and biological systems. 免费 open source GNU GPLv2 or later CP2K
Culgi 是 是 是 是 是 否 是 是 否 Atomistic and coarse-grained simulations, mesoscale methods, COSMO-RS and UNIFAC, database integration, mapping techniques, AM1 and interface to MOPAC/NWChem 专有 商业软件, gratis academic education Culgi BV
Desmond 是 是 是 是 否 是 否 否 是 High performance MD; has comprehensive GUI to build, visualize, and review results and calculation setup up and launch 专有, 商业软件 or gratis D. E. Shaw Research Schrödinger
DFTB+ 否 否 是 否 否 否 否 否 否 A fast and efficient versatile quantum mechanical simulation software package. Using DFTB+ you can carry out quantum mechanical simulations similar to density functional theory but in an approximate way, typically gaining around two orders of magnitude in speed. 免费 open source GNU LGPL [1]
Discovery Studio 是 是 是 是 是 否 是 是 否 Comprehensive life science modeling and simulation suite of applications focused on optimizing drug discovery process: small molecule simulations, QM-MM, pharmacophore modeling, QSAR, protein-ligand docking, protein homology modeling, sequence analysis, protein-protein docking, antibody modeling, etc. 专有, trial available Dassault Systèmes BIOVIA
(formerly Accelrys)
DL_POLY 否 是 是 是 否 否 I 否 否 DL_POLY is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov and W. Smith. It is part of the DL_Software suite of projects including DL_MESO (DPD), DL_FIELD (FF builder), ChemShell (QMMM environment), etc. 专有 商业软件, free source for academic use DL_POLY
Energy Calculation and Dynamics (ENCAD) 否 否 否 是 否 否 否 否 否 Notably the first MD simulation software by Michael Levitt 免费 open source [2]
fold.it Y / I 是 是 是 是 是 I 否 否 University of Washington and The Baker Labs; structure prediction, protein folding 专有, 商业软件 or gratis fold.it download page
FoldX I 是 是 否 否 否 否 否 否 Energy calculations, protein design 专有, 商业软件 or gratis CRG
GOMC 否 否 否 否 是 是 否 否 是 GPU Optimized Monte Carlo. Atomistic simulation engine, capable of simulating complex systems. 免费 opensource.GNU Affero General Public License. GOMC website. GOMC Github
GPIUTMD I I 是 是 否 I 否 否 是 Performs general purpose particle dynamics simulations on a single workstation, exploiting NVIDIA CUDA GPUs 专有 http://gpiutmd.iut.ac.ir
GROMACS 否 否 是 是 否[4] 是 I 是[5] 是 High performance MD 免费 open source GNU GPL gromacs.org
GROMOS 否 否 是 是 是 是 否 是 是 Intended for biomolecules 专有, commercial GROMOS website
GULP 否 否 是 是 否 否 否 否 否 Molecular dynamics and lattice optimization 专有, free academic use https://web.archive.org/web/20110604021055/http://projects.ivec.org/gulp/
HOOMD-blue 否 否 是 是 是 否 否 否 是 General-purpose molecular dynamics highly optimized for GPUs, includes various pair potentials, Brownian dynamics, dissipative particle dynamics, rigid body constraints, energy minimizing, etc. 免费 open source http://glotzerlab.engin.umich.edu/hoomd-blue/
HyperChem 是 是 是 是 是 否 是 是 否 De Facto Standard Molecular Modeling System 专有 Hypercube, Inc.
ICM 是 是 是 否 是 否 I 是 否 Powerful global optimizer in an arbitrary subset of internal variables, NOEs, docking (protein, ligand, peptide), EM, density placement 专有 Molsoft
LAMMPS 是 是 是 是 是 是 I 是 是 Has potentials for soft and solid-state materials and coarse-grain systems 免费 open source, GNU GPLv2 Sandia
MacroModel 是 是 是 是 是 否 I 是 否 OPLS-AA, MMFF, GBSA solvent model, conformational sampling, minimizing, MD. Includes the Maestro GUI which provides visualizing, molecule building, calculation setup, job launch and monitoring, project-level organizing of results, access to a suite of other modelling programs. 专有 Schrödinger
MAPS 是 是 是 是 是 是 是 否 是 Building, visualizing, and analysis tools in one user interface, with access to multiple simulation engines 专有, trial available Scienomics
Materials Studio 是 是 是 是 是 否 是 是 是 Environment that brings materials simulation technology to desktop computing, solving key problems in R&D processes 专有, trial available Dassault Systèmes BIOVIA
(formerly Accelrys)
MBN Explorer[6] + MBN Studio 是 是 是 是 是 否 否 是 是 Standard and reactive CHARMM force fields; molecular modeler (carbon nanomaterials, biomolecules, nanocrystals); explicit library of examples 专有, free trial available MBN Research Center
MedeA 是 是 是 是 是 否 是 否 否 Combines leading experimental databases and major computational programs like the Vienna Ab-initio Simulation Package (VASP), LAMMPS, GIBBS with sophisticated materials property prediction, analysis, visualizing 专有, trial available Materials Design
MCCCS Towhee 否 否 否 否 是 否 否 否 否 Originally designed to predict fluid phase equilibria 免费 open source GNU GPL Towhee Project
MDynaMix 否 否 否 是 否 否 否 否 否 Parallel MD 免费 open source GNU GPL Stockholm University
MOE 是 是 是 是 否 否 I 是 否 Molecular Operating Environment (MOE) 专有 Chemical Computing Group
MOIL 是 是 是 是 否 是 否 否 是 Includes action-based algorithms (stochastic difference equations in time, length) and locally enhanced sampling 免费 open source, public domain, source code MOIL
MolMeccano 否 是 否 否 否 否 否 否 否 Semi-automatic Force Field parametrizer 专有 MolMeccano Project
Orac 否 否 是 是 否 是 否 是 否 Molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomic level 免费 open source Orac download page
NAB[7] 否 是 否 否 否 否 否 否 否 Generates models for unusual DNA and RNA 免费 open source Case group
NAMD + VMD 是 是 是 是 否 是 I 是 是 Fast, parallel MD, CUDA 专有, free academic use, source code Beckman Institute
NWChem 否 否 是 是 否 否 是 否 否 High-performance computational chemistry software, includes quantum mechanics, molecular dynamics and combined QM-MM methods 免费 open source, Educational Community License version 2.0 NWChem
Packmol 否 是 否 否 否 否 否 否 否 Builds complex initial configurations for molecular dynamics 免费 open source GNU link
Prime 是 是 是 否 是 否 I 是 否 Homology modeling, loop and side chain optimizing, minimizing, OPLS-AA, SGB solvent model, parallalized 专有 Schrödinger
Protein Local Optimization Program 否 是 是 是 是 否 否 否 否 Helix, loop, and side chain optimizing, fast energy minimizing 专有 PLOP wiki
Q 否 否 否 是 否 否 否 否 否 (I) Free energy perturbation (FEP) simulations, (II) empirical valence bond (EVB), calculations of reaction free energies, (III) linear interaction energy (LIE) calculations of receptor-ligand binding affinities Uppsala Molekylmekaniska HB Q
RedMD[8] I 是 是 是 是 否 否 否 否 Reduced MD, package for coarse-grained simulations 免费, open source GNU University of Warsaw, ICM
SAMSON 是 是 是 是 否 否 是 否 否 Computational nanoscience (life sciences, materials, etc.). Modular architecture, modules termed SAMSON Elements 专有, gratis SAMSON Connect
StruMM3D (STR3DI32) 是 是 是 是 否 否 否 否 否 Sophisticated 3-D molecule builder and viewer, advanced structural analytical algorithms, full featured molecular modeling and quantitation of stereo-electronic effects, docking, and handling of complexes. 专有, free 200 atom version Exorga, Inc.
Scigress 是 是 是 是 否 否 是 是 否 MM, DFT, semiempirical methods, parallel MD, conformational analysis, Linear scaling SCF, docking protein-ligand, Batch processing, virtual screening, automated builders (molecular dynamics, proteins, crystals) 专有 SCIGRESS.com
Spartan 是 是 是 否 是 否 是 是 否 Small molecule (< 2,000 a.m.u.) MM and QM tools to determine conformation, structure, property, spectra, reactivity, and selectivity. 专有, free trial available Wavefunction, Inc.
TeraChem 否 否 是 是 否 否 是 否 是 High performance GPU-accelerated ab initio molecular dynamics and TD/DFT software package for very large molecular or even nanoscale systems. Runs on NVIDIA GPUs and 64-bit Linux, has heavily optimized CUDA code. 专有, trial licenses available PetaChem LLC
TINKER I 是 是 是 是 I I 是 是 Software tools for molecular design-Tinker-OpenMM[9]

Software tools for molecular design-Tinker-HP[10]

专有, gratis Washington University
Tremolo-X I 否 是 是 否 否 否 否 否 Fast, parallel MD 专有 Tremolo-X
UCSF Chimera 是 是 是 否 否 否 否 否 否 Visually appealing viewer, amino acid rotamers and other building, includes Antechamber and MMTK, Ambertools plugins in development. 专有, free academic use University of California
VEGA ZZ 是 是 是 I 是 否 否 是 是 3D viewer, multiple file format support, 2D and 3D editor, surface calculation, conformational analysis, MOPAC and NAMD interfaces, MD trajectory analysis, molecular docking, virtual screening, database engine, parallel design, OpenCL acceleration, etc. 专有, free academic use VEGA ZZ website
VLifeMDS 是 是 是 否 是 否 I 否 是 分子模拟软件Complete molecular modelling software, QSAR, combinatorial library generation, pharmacophore, cheminformatics, docking, etc. 专有 Vlife Sciences Technologies
WHAT IF 是 是 I I I 否 否 否 否 MD可视化工具，GROMACS的接口 专有 WHAT IF
YASARA 是 是 是 是 否 否 是 否 是 分子显示、建模、模拟 专有 YASARA.org

See also 编辑

参考资料 编辑

  1. ^ M. J. Harvey, G. Giupponi and G. De Fabritiis. ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale. Journal of Chemical Theory and Computation. 2009, 5 (6): 1632–1639. PMID 26609855. arXiv:0902.0827  . doi:10.1021/ct9000685. 
  2. ^ Johnston, MA, Fernández-Galván, I, Villà-Freixa, J. Framework-based design of a new all-purpose molecular simulation application: the Adun simulator. J. Comput. Chem. 2005, 26 (15): 1647–1659. PMID 16175583. doi:10.1002/jcc.20312. 
  3. ^ Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM Jr, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 1995, 117 (19): 5179–5197. CiteSeerX 10.1.1.323.4450  . doi:10.1021/ja00124a002. 
  4. ^ Harrison ET, Weidner T, Castner DG, Interlandi G. Predicting the orientation of protein G B1 on hydrophobic surfaces using Monte Carlo simulations. Biointerphases. 2017, 12 (2): 02D401. doi:10.1116/1.4971381. 
  5. ^ Implicit Solvent - Gromacs 互联网档案馆的存档，存档日期July 29, 2014，.
  6. ^ I.A. Solov'yov, A.V. Yakubovich, P.V. Nikolaev, I. Volkovets, A.V. Solov'yov. MesoBioNano Explorer - A universal program for multiscale computer simulations of complex molecular structure and dynamics. J. Comput. Chem. 2012, 33 (30): 2412–2439. PMID 22965786. doi:10.1002/jcc.23086. 
  7. ^ Macke T, Case DA. Modeling unusual nucleic acid structures. Molecular Modeling of Nucleic Acids. 1998: 379–393. 
  8. ^ A. Górecki; M. Szypowski; M. Długosz; J. Trylska. RedMD - Reduced molecular dynamics package. J. Comput. Chem. 2009, 30 (14): 2364–2373. PMID 19247989. doi:10.1002/jcc.21223. 
  9. ^ M. Harger, D. Li, Z. Wang, K. Dalby, L. Lagardère, J.-P. Piquemal, J. Ponder, P. Ren. Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs. Journal of Computational Chemistry. 2017, 38 (23): 2047–2055. PMC 5539969  . PMID 28600826. doi:10.1002/jcc.24853. 
  10. ^ L. Lagardère,L.-H. Jolly, F. Lipparini, F. Aviat, B. Stamm, Z. F. Jing, M. Harger, H. Torabifard, G. A. Cisneros, M. J. Schnieders, N. Gresh, Y. Maday, P. Y. Ren, J. W. Ponder, J.-P. Piquemal. Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields. Chemical Science. 2018, 9 (4): 956–972. PMC 5909332  . PMID 29732110. doi:10.1039/C7SC04531J. 

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