User:Njzjz/分子力学建模软件比较

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	蒙地卡羅方法	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^{[永久失效連結]}
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

参考资料

^ 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.
^ 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.
^ 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.
^ 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.
^ Implicit Solvent - Gromacs 互联网档案馆的存檔，存档日期July 29, 2014，.
^ 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.
^ Macke T, Case DA. Modeling unusual nucleic acid structures. Molecular Modeling of Nucleic Acids. 1998: 379–393.
^ 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.
^ 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.
^ 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.

外部链接

[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 互联网档案馆的存檔，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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See also

参考资料

外部链接