用户:Njzjz/分子力学建模软件比较
外观
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 | 注释 | 软件许可证 | 网站 |
---|---|---|---|---|---|---|---|---|---|---|---|---|
Abalone | 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 | 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]- Car–Parrinello molecular dynamics
- Comparison of force field implementations
- Comparison of nucleic acid simulation software
- List of molecular graphics systems
- List of protein structure prediction software
- List of quantum chemistry and solid state physics software
- List of software for Monte Carlo molecular modeling
- List of software for nanostructures modeling
- Molecular design software
- Molecular dynamics
- Molecular modeling on GPUs
- Molecule editor
参考资料
[编辑]- ^ 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 互联网档案馆的存档,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.