Comparison of software for molecular mechanics modeling

Short description: None

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

* GPU – GPU accelerated
* I – Has interface
* Imp – Implicit water
* MC – Monte Carlo
* MD – Molecular dynamics
* Min – Optimization
* QM – Quantum mechanics
* REM – Replica exchange method

Name  | View 3D | Model builder  | Min  | MD  | MC  | REM  | QM  | Imp  | GPU | Comments  | License | Website

|
|
|
|
|
|
|
|
|
|
|
|

ACEMD | No  | No  | Yes  | Yes  | Yes  | Yes  | No  | Yes  | Yes  | High Performance molecular dynamic simulation software  | Proprietary, Free for 1 GPU  | ACEMD
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
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  | No  | 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  | No  | 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
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
YASARA | Yes  | Yes  | Yes  | Yes  | No  | No  | Yes  | No  | Yes  | Molecular graphics, modeling, simulation  | Proprietary | YASARA.org

## See also

* 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

## Notes and references

1. ↑ "Citations for Amber" (in en). https://ambermd.org/CiteAmber.php.
2. ↑ "Predicting the orientation of protein G B1 on hydrophobic surfaces using Monte Carlo simulations". Biointerphases 12 (2): 02D401. 2017. doi:10.1116/1.4971381. PMID 27923271.
3. ↑ Implicit Solvent – Gromacs
4. ↑ "MAPS". http://www.scienomics.com/software/.
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.
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. PMID 28600826.
7. ↑ L. Lagardère; L.-H. Jolly; F. Lipparini; F. Aviat; B. Stamm; Z. F. Jing; M. Harger; H. Torabifard et al. (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. PMID 29732110.

## External links

* SINCRIS
* Linux4Chemistry
* Collaborative Computational Project
* World Index of Molecular Visualization Resources
* Short list of Molecular Modeling resources
* OpenScience
* Biological Magnetic Resonance Data Bank
* Materials modelling and computer simulation codes
* A few tips on molecular dynamics
* atomistic.software - atomistic simulation engines and their citation trends

* v
* t
* e

Computer simulation software

Biology|

* Protein structure prediction
* Nucleic acid simulation

Chemistry|

* Quantum chemistry
* Molecular modeling
* Monte Carlo molecular modeling
* Molecular design

Physics|

* Finite element
* Cosmological simulation

0.00

(0 votes)

|

Retrieved from "https://handwiki.org/wiki/index.php?title=Physics:Comparison_of_software_for_molecular_mechanics_modeling&oldid=660515"
*[v]: View this template
*[t]: Discuss this template
*[e]: Edit this template