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Comparison of software for molecular mechanics modeling

From Wikipedia - Reading time: 9 min

This is a list of computer programs that are predominantly used for molecular mechanics calculations.

Name View 3D Model builder Min MD MC REM QM Imp GPU Comments License Website
AMBER[1] No Yes Yes Yes Yes Yes I Yes Yes High Performance MD, Comprehensive analysis tools Proprietary, Free open source AMBER MD
Abalone Yes Yes Yes Yes Yes Yes I Yes Yes Biomolecular simulations, protein folding. Proprietary, gratis, commercial Agile Molecule
ADF Yes Yes Yes Yes Yes No Yes Yes Yes Modeling suite: ReaxFF, UFF, QM-MM with Amber and Tripos force fields, DFT and semi-empirical methods, conformational analysis with RDKit; partly GPU-accelerated Proprietary, commercial, gratis trial SCM
Ascalaph Designer Yes Yes Yes Yes Yes Yes I Yes Yes Molecular building (DNA, proteins, hydrocarbons, nanotubes), molecular dynamics, GPU acceleration Mixed: free open source (GNU GPL) & commercial Ascalaph Project
Avogadro Yes Yes Yes No No No I No No Molecule building, editing (peptides, small molecules, crystals), conformational analysis, 2D/3D conversion; extensible interfaces to other tools Free open source GNU GPL Avogadro
BOSS No No Yes No Yes No Yes No No OPLS Proprietary Yale University
CHARMM No Yes Yes Yes Yes I I Yes Yes Commercial version with multiple graphical front ends is sold by BIOVIA (as CHARMm), formerly Accelrys. Proprietary, commercial charmm.org
CHEMKIN No No No No No No No No No Chemical reaction kinetics. Proprietary CHEMKIN
CP2K No No Yes Yes Yes No Yes Yes Yes CP2K can perform atomistic and molecular simulations of solid state, liquid and biological systems. Free open source GNU GPLv2 or later CP2K
Desmond Yes Yes Yes Yes No Yes No No Yes High performance MD; has comprehensive GUI to build, visualize, and review results and calculation setup up and launch Proprietary, commercial or gratis D. E. Shaw Research Schrödinger
Discovery Studio Yes Yes Yes Yes Yes No Yes Yes Yes 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. Proprietary, trial available Dassault Systèmes BIOVIA
(formerly Accelrys)
fold.it Y / I Yes Yes Yes Yes Yes I No No University of Washington and The Baker Labs; structure prediction, protein folding Proprietary, commercial or gratis fold.it download page Archived 2011-04-04 at the Wayback Machine
FoldX I Yes Yes No No No No No No Energy calculations, protein design Proprietary, commercial or gratis CRG
GROMACS No No Yes Yes No[2] Yes I Yes[3] Yes High performance MD Free open source GNU GPL gromacs.org
GROMOS No No Yes Yes Yes Yes Yes Yes Yes Intended for biomolecules Proprietary, commercial GROMOS website
LAMMPS Yes Yes Yes Yes Yes Yes I Yes Yes Has potentials for soft and solid-state materials and coarse-grain systems Free open source, GNU GPLv2 Sandia
MacroModel Yes Yes Yes Yes Yes No I Yes No 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. Proprietary Schrödinger
MAPS[4] Yes Yes Yes Yes Yes Yes Yes No Yes Building, visualizing, and analysis tools in one user interface, with access to multiple simulation engines Proprietary, trial available Scienomics
Materials Studio Yes Yes Yes Yes Yes No Yes Yes Yes Environment that brings materials simulation technology to desktop computing, solving key problems in R&D processes Proprietary, trial available Dassault Systèmes BIOVIA
(formerly Accelrys)
MBN Explorer[5] + MBN Studio Yes Yes Yes Yes Yes No No Yes Yes Standard and reactive CHARMM force fields; molecular modeler (carbon nanomaterials, biomolecules, nanocrystals); explicit library of examples Proprietary, free trial available MBN Research Center
MDynaMix No No No Yes No No No No No Parallel MD Free open source GNU GPL Stockholm University
MOE Yes Yes Yes Yes No No I Yes No Molecular Operating Environment (MOE) Proprietary Chemical Computing Group
ms2 Yes Yes Yes Yes Yes No No No No direct on the fly computation of large number of thermophysical properties. Main application of ms2 is on fluids. Free open source ms-2.de
OpenMM No No Yes Yes Yes Yes No Yes Yes High Performance MD, highly flexible, Python scriptable Free open source MIT OpenMM
Orac No No Yes Yes No Yes No Yes No Molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomic level Free open source Orac download page
NAMD + VMD Yes Yes Yes Yes No Yes I Yes Yes Fast, parallel MD, CUDA Proprietary, free academic use, source code Beckman Institute
NWChem No No Yes Yes No No Yes No No High-performance computational chemistry software, includes quantum mechanics, molecular dynamics and combined QM-MM methods Free open source, Educational Community License version 2.0 NWChem
Protein Local Optimization Program No Yes Yes Yes Yes No No No No Helix, loop, and side chain optimizing, fast energy minimizing Proprietary PLOP wiki
Q No No No Yes No No No No No (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 Free open source GNU GPLv2 or later Q
QuantumATK Yes Yes Yes Yes Yes No Yes Yes Yes Complete atomistic modeling platform for material science. It includes DFT (Plane-Wave and LCAO), Semi-empirical, and Force Field simulation engines. Proprietary, commercial Synopsys QuantumATK
Quantum ESPRESSO No No Yes Yes No No Yes I Yes Open-source suite focused on electronic-structure calculations and MD (particularly CPMD), popular for its flexibility and extensive community support. Free open source GNU GPLv2 or later Quantum ESPRESSO
SAMSON Yes Yes Yes Yes No No Yes No No Computational nanoscience (life sciences, materials, etc.). Modular architecture, modules termed SAMSON Elements Proprietary, gratis SAMSON Connect
Scigress Yes Yes Yes Yes No No Yes Yes No MM, DFT, semiempirical methods, parallel MD, conformational analysis, Linear scaling SCF, docking protein-ligand, Batch processing, virtual screening, automated builders (molecular dynamics, proteins, crystals) Proprietary SCIGRESS.com
Spartan Yes Yes Yes No Yes No Yes Yes No Small molecule (< 2,000 a.m.u.) MM and QM tools to determine conformation, structure, property, spectra, reactivity, and selectivity. Proprietary, free trial available Wavefunction, Inc.
TeraChem No No Yes Yes No No Yes No Yes 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. Proprietary, trial licenses available PetaChem LLC
TINKER I Yes Yes Yes Yes I I Yes Yes Software tools for molecular design-Tinker-OpenMM[6]

Software tools for molecular design-Tinker-HP[7]

Proprietary, gratis Washington University
UCSF Chimera Yes Yes Yes No No No No No No Visually appealing viewer, amino acid rotamers and other building, includes Antechamber and MMTK, Ambertools plugins in development. Proprietary, free academic use University of California
VASP No No Yes Yes No Yes Yes I Yes Highly efficient DFT code often used in materials science providing excellent performance on large systems. Proprietary VASP
YASARA Yes Yes Yes Yes No No Yes No Yes Molecular graphics, modeling, simulation Proprietary YASARA.org

See also

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Notes and references

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  1. ^ "Citations for Amber". ambermd.org. Retrieved 2021-06-15.
  2. ^ Harrison ET, Weidner T, Castner DG, Interlandi G (2017). "Predicting the orientation of protein G B1 on hydrophobic surfaces using Monte Carlo simulations". Biointerphases. 12 (2): 02D401. doi:10.1116/1.4971381. PMC 5148762. PMID 27923271.
  3. ^ Implicit Solvent – Gromacs Archived July 29, 2014, at the Wayback Machine
  4. ^ "MAPS". Archived from the original on 2019-11-28. Retrieved 2016-11-14.
  5. ^ I.A. Solov'yov; A.V. Yakubovich; P.V. Nikolaev; I. Volkovets; A.V. Solov'yov (2012). "MesoBioNano Explorer - A universal program for multiscale computer simulations of complex molecular structure and dynamics". J. Comput. Chem. 33 (30): 2412–2439. doi:10.1002/jcc.23086. PMID 22965786. S2CID 22553279.
  6. ^ M. Harger; D. Li; Z. Wang; K. Dalby; L. Lagardère; J.-P. Piquemal; J. Ponder; P. Ren (2017). "Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs". Journal of Computational Chemistry. 38 (23): 2047–2055. doi:10.1002/jcc.24853. PMC 5539969. PMID 28600826.
  7. ^ 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 (2018). "Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields". Chemical Science. 9 (4): 956–972. doi:10.1039/C7SC04531J. PMC 5909332. PMID 29732110.
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