Amber Molecular Dynamics Software

Minor Version: 8.4.4 (May 1, 2018) Introduction The Tinker molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. Tinker has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98, ff99, ff99SB), CHARMM (19, 22, 22/CMAP). 63 rows Comparison of software for molecular mechanics modeling Jump to navigation Jump to.

AMBER Molecular Dynamics

Contents

AMBER Roll

This roll installs AMBER tools.There are 4 flavors compiled for each compiler (gnu, intel):

Amber is a licensed software. Get licensed files for AMBAER and AmberTools fromAmarolab and save copy in nbcr.ucsd@gmail.com accountDownload the appropriate amber source files into the src/amber.Download the benchmark suite in src/amber-test:

Dependencies

The mpi roll must be installed on the build/install host.depends on mpi libraries.
The intel roll must be installed on the build/install host. In the absence of intel compilerthe roll should be buld with ROLLCOMPILEr='gnu'.
The cuda roll must be installed on build/install host . In the absence of cuda, editsrc/amber/Makefile targets to remove cuda-specific compilation.
The roll sources assumes that modulefiles provided by intel, cuda and mpirolls are available.

The roll uses openmpi compiled with intel and gnu compilers for eth fabric.To make a roll use the following command:

A successful build will create the file amber-*.disk1.iso.

To install, execute these instructions on a Rocks frontend:

Tthe roll installs amber and environment module files in:

For Sep 2015 workshop buid amberGaMD roll based on a received patch for amber14 sourceCreate the following changes to the roll source:

See diffs for the above files in GaMD-diffs file at the top of the roll.After creating changes build amberGaMD roll

Testing

A test script amber.t can be run to verify properinstallation of the roll binaries and module files. Torun the test scripts execute the following command(s):

A benchmark suit distro (from Amber site) contains a shell script run_bench_CPU+GPU.shand required input to run suite of tests. Untar, adjust cpu and gpu counts in the scriptfor a specific host.

(Redirected from List of software for molecular mechanics modeling)

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
Abalone	Yes	Yes	Yes	Yes	Yes	Yes	I	Yes	Yes	Biomolecular simulations, protein folding.	Proprietary, gratis, commercial	Agile Molecule
ACEMD^[1]	No	No	Yes	Yes	No	Yes	No	No	Yes	Molecular dynamics with CHARMM, Amber forcefields; runs on NVIDIA GPUs, highly optimized with CUDA	Proprietary, gratis and commercial versions	Acellera Ltd^{[permanent dead link]}
ADF	Yes	Yes	Yes	Yes	No	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
ADUN^[2]	No	No	Yes	Yes	No	No	Yes	Yes	Yes	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	Free open sourceGNU GPL	https://web.archive.org/web/20160303133843/https://gna.org/projects/adun
Assisted Model Building with Energy Refinement (AMBER)^[3]	No	Yes	Yes	Yes	No	Yes	I	Yes	Yes	?	Proprietary	ambermd.org
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
Automated Topology Builder (ATB)	Yes	Yes	Yes	No	No	No	No	No	No	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	Proprietarycommercial, gratis academic use	Automated Topology Builder
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 sourceGNU 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 Accelrys (as CHARMm)	Proprietary, commercial	charmm.org
ChemDoodle 3D	Yes	Yes	Yes	No	No	No	No	No	No	Intuitive building of molecules in real-time; production of high quality publication graphics; works on Windows, macOS and Linux; developed by iChemLabs	Proprietary, commercial, free trial	ChemDoodle 3D Website
CHEMKIN	No	No	No	No	No	No	No	No	No	Chemical reaction kinetics.	Proprietary	CHEMKIN
COSMOS	Yes	Yes	Yes	Yes	Yes	No	I	No	No	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	Proprietary, commercial, free without GUI	COSMOS Software
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 sourceGNU GPLv2 or later	CP2K
Culgi	Yes	Yes	Yes	Yes	Yes	No	Yes	Yes	No	Atomistic and coarse-grained simulations, mesoscale methods, COSMO-RS and UNIFAC, database integration, mapping techniques, AM1 and interface to MOPAC/NWChem	Proprietarycommercial, gratis academic education	Culgi BV
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
DFTB+	No	No	Yes	No	No	No	No	No	No	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.	Free open sourceGNU LGPL	[1]
Discovery Studio	Yes	Yes	Yes	Yes	Yes	No	Yes	Yes	No	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)
DL_POLY	No	Yes	Yes	Yes	No	No	I	No	No	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.	Proprietarycommercial, free source for academic use	DL_POLY
Energy Calculation and Dynamics (ENCAD)	No	No	No	Yes	No	No	No	No	No	Notably the first MD simulation software by Michael Levitt	Free open source	[2]
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
GOMC	No	No	No	No	Yes	Yes	No	No	Yes	GPU Optimized Monte Carlo. Atomistic simulation engine, capable of simulating complex systems.	Free opensource.GNU Affero General Public License.	GOMC website. GOMC Github
GPIUTMD	I	I	Yes	Yes	No	I	No	No	Yes	Performs general purpose particle dynamics simulations on a single workstation, exploiting NVIDIA CUDA GPUs	Proprietary	http://gpiutmd.iut.ac.ir
GROMACS	No	No	Yes	Yes	No^[4]	Yes	I	Yes^[5]	Yes	High performance MD	Free open sourceGNU GPL	gromacs.org
GROMOS	No	No	Yes	Yes	Yes	Yes	No	Yes	Yes	Intended for biomolecules	Proprietary, commercial	GROMOS website
GULP	No	No	Yes	Yes	No	No	No	No	No	Molecular dynamics and lattice optimization	Proprietary, free academic use	http://gulp.curtin.edu.au/gulp/
HOOMD-blue	No	No	Yes	Yes	Yes	No	No	No	Yes	General-purpose molecular dynamics highly optimized for GPUs, includes various pair potentials, Brownian dynamics, dissipative particle dynamics, rigid body constraints, energy minimizing, etc.	Free open source	http://glotzerlab.engin.umich.edu/hoomd-blue/
HyperChem	Yes	Yes	Yes	Yes	Yes	No	Yes	Yes	No	De Facto Standard Molecular Modeling System	Proprietary	Hypercube, Inc.
ICM	Yes	Yes	Yes	No	Yes	No	I	Yes	No	Powerful global optimizer in an arbitrary subset of internal variables, NOEs, docking (protein, ligand, peptide), EM, density placement	Proprietary	Molsoft
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^[6]	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^[7] + 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
MedeA	Yes	Yes	Yes	Yes	Yes	No	Yes	No	No	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	Proprietary, trial available	Materials Design
MCCCS Towhee	No	No	No	No	Yes	No	No	No	No	Originally designed to predict fluid phase equilibria	Free open sourceGNU GPL	Towhee Project
MDynaMix	No	No	No	Yes	No	No	No	No	No	Parallel MD	Free open sourceGNU GPL	Stockholm University
MOE	Yes	Yes	Yes	Yes	No	No	I	Yes	No	Molecular Operating Environment (MOE)	Proprietary	Chemical Computing Group
MOIL	Yes	Yes	Yes	Yes	No	Yes	No	No	Yes	Includes action-based algorithms (stochastic difference equations in time, length) and locally enhanced sampling	Free open source, public domain, source code	MOIL
MolMeccano	No	Yes	No	No	No	No	No	No	No	Semi-automatic Force Field parametrizer	Proprietary	MolMeccano Project
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
NAB^[8]	No	Yes	No	No	No	No	No	No	No	Generates models for unusual DNA and RNA	Free open source	Case group
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
Packmol	No	Yes	No	No	No	No	No	No	No	Builds complex initial configurations for molecular dynamics	Free open sourceGNU	link
Prime	Yes	Yes	Yes	No	Yes	No	I	Yes	No	Homology modeling, loop and side chain optimizing, minimizing, OPLS-AA, SGB solvent model, parallalized	Proprietary	Schrödinger
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	Uppsala Molekylmekaniska HB	Q
RedMD^[9]	I	Yes	Yes	Yes	Yes	No	No	No	No	Reduced MD, package for coarse-grained simulations	Free, open sourceGNU	University of Warsaw, ICM
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
StruMM3D (STR3DI32)	Yes	Yes	Yes	Yes	No	No	No	No	No	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.	Proprietary, free 200 atom version	Exorga, Inc.
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 performanceGPU-accelerated ab initiomolecular dynamics and TD/DFT software package for very large molecular or even nanoscale systems. Runs on NVIDIAGPUs and 64-bitLinux, 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^[10] Software tools for molecular design-Tinker-HP^[11]	Proprietary, gratis	Washington University
Tremolo-X	I	No	Yes	Yes	No	No	No	No	No	Fast, parallel MD	Proprietary	Tremolo-X
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
VEGA ZZ	Yes	Yes	Yes	I	Yes	No	No	Yes	Yes	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.	Proprietary, free academic use	VEGA ZZ website
VLifeMDS	Yes	Yes	Yes	No	Yes	No	I	No	Yes	Complete molecular modelling software, QSAR, combinatorial library generation, pharmacophore, cheminformatics, docking, etc.	Proprietary	Vlife Sciences Technologies
WHAT IF	Yes	Yes	I	I	I	No	No	No	No	Visualizer for MD, interface to GROMACS	Proprietary	WHAT IF
YASARA	Yes	Yes	Yes	Yes	No	No	Yes	No	Yes	Molecular graphics, modeling, simulation	Proprietary	YASARA.org

Notes and references[edit]

^M. J. Harvey, G. Giupponi and G. De Fabritiis (2009). 'ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale'. Journal of Chemical Theory and Computation. 5 (6): 1632–1639. arXiv:0902.0827. doi:10.1021/ct9000685. PMID26609855.
^Johnston, MA, Fernández-Galván, I, Villà-Freixa, J (2005). 'Framework-based design of a new all-purpose molecular simulation application: the Adun simulator'. J. Comput. Chem. 26 (15): 1647–1659. doi:10.1002/jcc.20312. PMID16175583.CS1 maint: multiple names: authors list (link)
^Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM Jr, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995). 'A second generation force field for the simulation of proteins, nucleic acids, and organic molecules'. J. Am. Chem. Soc. 117 (19): 5179–5197. CiteSeerX10.1.1.323.4450. doi:10.1021/ja00124a002.
^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. PMC5148762. PMID27923271.
^Implicit Solvent - GromacsArchived July 29, 2014, at the Wayback Machine
^MAPS
^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. PMID22965786.CS1 maint: uses authors parameter (link)
^Macke T, Case DA (1998). 'Modeling unusual nucleic acid structures'. Molecular Modeling of Nucleic Acids: 379–393.
^A. Górecki; M. Szypowski; M. Długosz; J. Trylska (2009). 'RedMD - Reduced molecular dynamics package'. J. Comput. Chem. 30 (14): 2364–2373. doi:10.1002/jcc.21223. PMID19247989.
^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. PMC5539969. PMID28600826.CS1 maint: multiple names: authors list (link)
^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. PMC5909332. PMID29732110.CS1 maint: multiple names: authors list (link)

Molecular Dynamics Pdf

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