Welcome to NetSci's
List of Molecular Mechanics and
Molecular Dynamics Software

Notice:Statements and opinions made for the products within this listing were supplied by their owners. Network Science Corporation assumes no responsibility for the content of these listings. All product and company names mentioned in this publication are patents, trademarks, registered trademarks or servicemarks of their respective holders. The Tabular Software Listings portion of this site are Copyright © 1995/2006 by Network Science Corporated. All rights reserved.

The Software Section of NetSci is accessed by hundreds of scientists every week. Our goal is to make this resource as comprehensive as possible. If your software program is not included, please send e-mail with a brief description, the categories under which your program should appear, the platforms supported, and contact information.

For programs currently listed in NetSci, please check the table and description and notify us of any changes or additions.

[ A, B, C ] -- [ D, E, F ] -- [ G, H, I ] -- [ J, K, L ]
[ M, N, O ] -- [ P, Q, R ] -- [ S, T, U ] --
[ V, W ] -- [ X, Y, Z]




--- A, B, C ---





 

Abalone is a program for molecular mechanics. Abalone primarily designed for proteins and nucleic acids simulations.





 

AMBER (Assisted Model Building using Energy Refinement). A suite of programs for molecular mechanics and molecular dynamics simulations. Designed primarily for proteins and nucleic acids.





 

AMMP is a fully featured molecular modeling program. It features:

  • Fast long range electrostatics and nonbonded terms. AMMP runs without cutoffs in times comparable to or better than an 8 Angstrom cutoff in other programs.

  • Stable, numerically accurate, molecular dynamics. AMMP is stable with difficult problems such as parallel stranded DNA.

  • Flexible choice of potential functions. In addition to standard formulations, AMMP has non-point charges, explicit Debye screening, accurate polarization models, non-harmonic bond and angle formulations, and coupled bond-angle terms available.

  • Calculates partial charges for new molecules.

  • Embeding and homotopy methods for rapid model building.

  • Self-contained, and can be embeded in other programs.

  • Highly parallel version available with PVM,

  • Literature citations for AMMP.

AMMP is extensively vectorized and runs under UNIX, WINDOWS 3.1 and WINDOWS 95. The program and a full description on its use is available at the ammp page





 

Biomer features include biopolymer model builders (nucleic acids, proteins, and polysaccharides), AMBER force-field based geometry optimization, an interactive molecule editor, and simulated annealing with molecular dynamics. Biomer is located at

http://www.scripps.edu/~nwhite/Biomer/index.html

Biomer should run on all platforms that support java and/or have a current java-enabled web browser. Contact:

Neill K. White
The Scripps Research Institiute
10550 North Torrey Pines Rd.
La Jolla, CA 92037
(619) 784-9620




 

BOSS (Biochemical and Organic Simulation System). Monte Carlo statistical mechanics simulations of organic molecules, complexes and reactions in solution.





 

Cerius2 is a software environment designed to facilitate the chemical computing needs of R&D organizations. With Cerius2, scientists are able to apply the predictive power of computational chemistry to the critical issues in their research. WIth Cerius2 users can visualize structures, predict the properties and behavior of chemical systems, refine structural models, and integrate in-house computational codes in a commercial software environment. The Cerius2 environment integrates builder modules, development tools, force fields, simulation and visualization tools with tools specifically developed for applications in the life and materials sciences. Biopolmer modeling components include:

  • C2*Minimizer predicts low-energy structures using molecular mechanics calculations and the power of Cerius2 Open Force Field, which helps you gain increased understanding of molecular, macromolecular, amorphous, crystalline, and surface structure and properties.

  • C2*Dynamics applies molecular mechanics to study structure relaxation and investigate the behavior of a material over a time period. Properties that can be deduced include: stability, diffusion, radial distribution functions and structure factors, and velocity auto-correlation functions.

  • C2*FFE (Force Field Editor) helps you adapt force fields from the Cerius2 database or create your own. You can apply force fields from the literature to your problems and develop and validate in-house parameterizations.

  • C2*MMFF provides specialists access to the Merck Molecular Force Field for accurately studying the structure, energetics, and dynamics of molecular systems in the life sciences. MMFF is broadly parameterized for organic and bio-organic systems and for the intermolecular interactions crucial to enzyme binding.

  • C2*OFF (Open Force Field) provides molecular mechanics force fields to support Cerius2 property prediction modules. You can choose from an extensive database of force fields covering organics, polymers, zeolites, organometallics, and other materials types.




 

CHARMm (Chemistry at HARvard, Macromolecular mechanics) is a highly regarded and widely used simulation package. CHARMm combines standard minimization and dynamics capabilities with expert features including free energy perturbation (FEP), correlation analysis and combined quantum, and molecular mechanics (QM/MM) methods. Simulations provide insight into molecular-level structure, interactions, and energetics. Academic program (CHARMM) is available from

Martin Karplus
Department of Chemistry
Harvard University
12 Oxford Street
Cambridge, MA 02138, USA
Tel: (617)495-4018
Fax: (617)495-1792
E-mail: karplus@huche1.bitnet




--- D, E, F ---





 

Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms containing a large number of processors, but may also be executed on a single computer. Desmond and its source code are available without cost for non-commercial use by universities and other not-for-profit research institutions.





 

Discover is a simulation program available within Insight II. It incorporates a range of well validated forcefields for dynamics simulations, minimization, and conformational searches, allowing you to predict the structure, energetics and properties of organic, inorganic, organometallic, and biological systems. Discover also implements IPC (Inter Process Communications), which allows users to instruct Discover to turn processing control over to external programs, and retrieve the results, incorporating the results into the continuing Discover computations. Modules within Discover include:

  • CFF95, an advanced Class II Force field, is used to optimize DNA, RNA, carbohydrates, lipids, proteins, peptides, and small-molecule models, giving a high confidence level for calculations in drug discovery, protein design, genomic therapeutics, NMR spectroscopy, and X-ray crystallography.

  • DeCipher is a powerful and flexible program for high-level analysis of molecular structure and the results of molecular dynamics simulations.




 

Dynama is a fast docking program which uses the FFT to calculate the interaction energy between two molecules without cutoffs or other aphysical approximations. Dynama is able to treat flexability in the ligands. Dynama can approximations to the the partition function so that free energies of solvation and solvent exclusion effects can be included in a screening calculation. The program is available at the ammp page http://www.cs.gsu.edu/~cscrwh/progs/progs.html.





 

ECEPP (Empirical Conformational Energy Program for Peptides) is a molecular mechanics based conformational searching program for proteins and peptides. Contact: Harold Scheraga, Baker Laboratory of Chemistry, Cornell University, Ithaca, NY 14853-1301 USA, Tel:+1 607-255-4034, Fax: +1 607-255-4137, E-mail: mvw@cornellc.bitnet The program is also available from QCPE





 

FANTOM The main purpose of the program FANTOM (Fast Newton - Raphson Torsion Angle Minimizer) is the calculation of conformations of linear and cyclic polypeptides and proteins with low conformational energies including distance and dihedral angle constraints from nuclear magnetic resonance experiments or for modeling purposes. The user can run energy minimizations and/or Monte Carlo simulations of an empirical energy function. Protein-solvent interaction is included with a fast routine for the calculation of accessible surface areas of individual atoms and their gradients. FANTOM is also suited for the exploration of low energy conformations of cyclic peptides or flexible loops in proteins.

FANTOM is available from the Sealy Center for Structural Biology, University of Texas Medical Branch. Program home page: http://www.scsb.utmb.edu/fantom/fm_home.html

Contact person: prof. Werner Braun, (E-mail: werner@tocsy.utmb.edu; phone: (409) 747-6810).





--- G, H, I ---





 

gOpenMol Scarecrow Computing is pleased to announce the availability of the gOpenMol program for the display and analysis of molecular systems. The program is available for anybody interested. There is no time limit set for the usage of the program but that remember it's an alpha version.

This first release is only for the Windows 95/NT platforms. You will also need at least 16 MB of memory (32 MB is recommended) and preferable at least 64 Kcolours. I also recommend that you have the service packs (up to SP3) for NT installed because this service pack fixes a bug in the Microsoft OpenGL implementation.

Information about gOpenMol is available at:

http://laaksonen.csc.fi/gopenmol/

The gOpenMol program is a rewrite of the old SCARECROW program. gOpenMol is now implemented using OpenGL and Tcl/Tk. This gives the user great flexibility to reconfigure almost the entire program.

Contact:

Leif Laaksonen
Center for Scientific Computing
P.O. Box 405
FIN-02101 Espoo, FINLAND
Tel: 358 9 4572378
Fax: 358 9 4572302
E-mail: Leif.Laaksonen@csc.fi




 

GROMACS 1.3 is a set of molecular dynamics code and analysis tools which is available from the GROMACS website Features of the software include:

  • The GROMACS code runs your simulations *blazingly fast* on all UNIX platforms. The code is especially well-tuned for pipelined architectures, such as MIPS R8000, HP:PA-RISC, Intel i860 etc.
  • Runs on parallel computers using either the MPI or PVM libraries.
  • Easy generation of topology etc. from pdb files
  • Conversion of GROMOS87 files
  • NMR Refinement using NOE restraints with time averaging and ensemble averaging
  • Many analysis tools, including trajectory viewer
  • 200 page User Manual available in PostScript
  • Special compressed trajectory format to reduce disk usage. This file format is supported by the WhatIF software.
  • * FREE * for academic institutions. Commercial license may be requested for a fee.




 

GROMOS (GROningen MOlecular Simulation package) is a molecular mechanics and dynamics program developed by W. F. van Gunsteren and co-workers at The University of Groningen. Contact:

Biomos B. V.
Laboratory of Physical Chemistry
University of Groningen
Nijenborgh 16, 9747 AG Groningen, The Netherlands
Tel: +31-50-63-4329
Fax: +31-50-634200




--- J, K, L ---





 

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is an open source program for molecular mechanics and dynamics on a variety of molecular systems. LAMMPS is distributed by Sandia National Laboratories, a US Department of Energy laboratory.





--- M, N, O ---





 

MD-Display is designed to allow creation of colored, animated displays of the data produced by a molecular dynamics program. Rotation, clipping, translation, coloring and scaling are controlled through the mouse and keyboard. Additional display features include stereo, half-bond coloring, control of animation speed and direction. Allows user to monitor distances, bond angles, dihedrals and hydrogen bonds during animation. Other display options include solvent accessible surfaces (static), Ramachandran plots, frequency filtering of trajectories in real time, generation of PostScript files. NM Display is available for visualization of normal mode displacements. The programs were developed by T. Callahan, E. Swanson and T.P. Lybrand and are available as program number 623 from QCPE for Silicon Graphics 4D GT, GTX, Personal Iris and Indigo workstations.

Version 3 is now multi-platform and available at: http://www.structbio.vanderbilt.edu/~cmoth/mddisplay



 

MDScope is an integrated set of computational tools which functions as an interactive visual computing environment for the simulation and study of biopolymers. The project implements standard visualization and simulation methods and offers a foundation for testing new algorithms and capabilities. Three major software components. (The programs can be used together or independently.)

  1. VMD (Visual Molecular Dynamics) is program for interactive display and animation of molecules; It runs on Silicon Graphics workstations and may be compiled for HP-UX workstations if the NPGL library is available. Full source code and binaries for SGI's running IRIX 5.X are included in the distribution. See WWW page for details at URL: http://www.ks.uiuc.edu/Research/vmd/.

  2. NAMD (Not (just) Another Molecular Dynamics program) is a MD program designed for the simulation of large biomolecular systems on distributed memory machines. It is written in C++ in a modular fashion so that new algorithms may be readily tested. See WWW page for details at URL: http://www.ks.uiuc.edu/Research/namd/

  3. MDComm is a set of communications routines and programs which exchanges simulation data and interactive forces between NAMD and VMD. It is built on the RAPP software package (developed by Rick Kufrin at NCSA), which simplifies the process of building and maintaining interactive client/server applications. See WWW page for details at URL: http://www.ks.uiuc.edu/Research/mdcomm/




 

MM2, MM3, MM4 are molecular mechanics programs used to optimize geometry, determine thermodynamic values and IR spectral data. MM2/MM3/MM4 are available from Tripos, Inc.





 

MOIL-View is a program for SGI and IBM RS/6000 workstations designed to allow the user to view and analyze molecular structures and dynamics.





 

MOLDY is a molecular dynamics simulation program for solids and liquids. It will handle atoms, ions and rigid molecules, but is currently limited to pairwise central forces.





 

MOLDYN is an interactive general-purpose program for calculation and evaluation of data from molecular dynamics. Written by Kumar, Craik and Levy. It is available as program number 489 from QCPE





 

MOLSCAT is a code for quantum mechanical (coupled channel) solution of the nonreactive molecular scattering problem. Code is implemented for various types of collision partners. In addition to the essentially exact close coupling method several approximate methods, including the Coupled States and Infinite Order Sudden approximations, are provided. The code is in near standard FORTRAN 77 and has been ported to a large number of platforms. The source code supplied was run at this site on an IBM RS/6000 and also on IBM and compatible mainframes. It should work on most other machines; for the Cray, however, modifications to run in single precision should be made.





 

MORATE (Molecular Orbital RATE calculations) is a set of FORTRAN subprograms and Unix scripts for interfacing the POLYRATE dynamics program and the MOPAC electronic structure program for the purpose of direct dynamics calculations of gas-phase chemical reaction rates of polyatomic species (and also atoms and diatoms as special cases) using semiempirical molecular orbital theory to represent the potential energy of interaction and using POLYRATE for the dynamics. The interface is based on the POLYRATE hooks protocol. The dynamics methods used are variational or conventional transition state theory and multidimensional semiclassical approximations for tunneling and nonclassical reflection. Rate constants may be calculated by any of the methods available in the POLYRATE-version 7.9.1 program for canonical or microcanonical ensembles or for specific vibrational states of selected modes with translational, rotational, and other vibrational modes treated thermally. Bimolecular and unimolecular reactions are included. Both single-level and dual- level modes are available. In single-level mode, potential energies and gradients can be calculated by any of the semiempirical molecular orbital methods in the MOPAC version 5.07mn package, in particular PM3, AM1, MNDO, and MINDO/3, and also by the NDDO-SRP method. In dual-level mode, these options are available for the lower-level part of the calculation, and higher-level data is read from an external file.





 

MPA/MPG: Molecular Packing Analysis/Molecular Packing Graphics. Mpa/mpg is a suite of programs designed for molecular packing analysis and molecular packing graphics in the unix environment. The capability of the mpa module extends from minimization of the energy of association of two or more molecules (e.g., molecular clusters and host-substrate docking) to energy minimization of a molecular assembly in a crystal lattice of any space group symmetry (e.g., crystal polymorph prediction). The software is capable of predicting space groups and reduced cells in which a given molecule may crystallize. Provision for limited molecular flexibility is made through selected rotations about intramolecular bonds. Molecular and/or crystal symmetry restrictions may be selectively applied as desired.

A library of commonly available intermolecular force fields is included (e.g., WH86, MM85, Biosym, Charmm, Dreiding, etc.), and provision is made for user supplied force fields. The program selects energy minimization by OREM (off-ridge eigenvector minimization), SD (steepest descents), or NR (Newton-Raphson) as appropriate for the model. All first and second derivatives of the energy are calculated analytically; the second derivative matrix (hessian) is diagonalized and its eigenvectors determined. Simulated annealing is included to aid in locating global, rather than subsidiary, energy minima. The molecular packing graphics (mpg) module is closely integrated with the molecular packing analysis module to give users fast, convenient, and useful graphical visualization of the results.

The programs are available from:

Dr. Donald E. Williams
Department of Chemistry
University of Louisville
Louisville, KY 40292
phone:502-852-5975
fax: 502-852-8149
email: dewill01@homer.louisville.edu




 

namd is a new package for high performance parallel molecular dynamics simulations.





 

nbp (nonbonded potentials) is a software tool which derives an optimized force field from molecular crystal and/or molecular cluster data. Customized force fields can be developed and optimized from any training set of data. Nonbonded potential functions can be of either the (exp-6-1) or (n-6-1) type, including the possibility of non-atomic sites. A given element may be subdivided into several potential types. Input to the program is a set of any number of structures encoded in the mpa/mpg (molecular packing analysis/molecular packing graphics) format. The force field can also be scaled to one or more energies such as heats of sublimation or heats of association.

For further information contact:

Dr. Donald E. Williams
Department of Chemistry
University of Louisville
Louisville, KY 40292 USA
email: dewill01@homer.louisville.edu




--- P, Q, R ---





 

Packmol creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations.

The great variety of types of spatial constraints that can be attributed to the molecules, or atoms within the molecules, makes it easy to create ordered systems, such as lamellar, spherical or tubular lipid layers.

The user must provide only the coordinates of one molecule of each type, the number of molecules of each type and the spatial constraints that each type of molecule must satisfy.

The package is compatible with input files of PDB, TINKER, XYZ and MOLDY formats. Packmol is offered by

Leandro Martinez
Institute of Chemistry
State University of Campinas, Brazil
Home Page: http://www.ime.unicamp.br/~martinez/packmol




 

pmd (Parallel Molecular Dynamics) is an advanced parallel molecular dynamics program which allows the efficient inclusion of long-range Coulomb interactions using a fast multipole algorithm.





 

POLYRATE is a computer program for the calculation of chemical reaction rates of polyatomic species (and also atoms and diatoms as special cases). POLYRATE-version 8.0 is an enhanced version of POLYRATE with improved capabilities for direct dynamics and curvilinear coordinates. The methods used are variational or conventional transition state theory and multidimensional semiclassical approximations for tunneling and nonclassical reflection. Generalized transition state theory calculations may be carried out using either rectilinear coordinates, non-redundant curvilinear coordinates, or redundant curvilinear coordinates. Zero-curvature, centrifugal-dominant small-curvature, and large-curvature-version 3 (LC3) tunneling methods are included, including tunneling into excited states in the LC3 model, and optimized multidimensional tunneling is also included.

Rate constants may be calculated for canonical or microcanonical ensembles or for specific vibrational states of selected modes with translational, rotational, and other vibrational modes treated thermally. Bimolecular and unimolecular reactions and gas-phase, solid-state, and gas-solid-interface reactions are all included.

Potential energy surfaces may be analytic functions evaluated by subroutines, or they may be implicit surfaces defined by electronic structure input files containing energies, gradients, and force constants (Hessians) at selected points on a reaction path. The use of electronic structure calculations to calculate rate constants or other dynamical quantities without an analytic potential energy surface is called direct dynamics. Analytic surfaces may be used for variational transition state theory and any of the types of tunneling calculations, single-level and dual-level calculations based solely on electronic structure input files may be used for variational transition state theory and zero-curvature or small-curvature tunneling, and dual-level calculations based on using an analytic potential energy surface as the lower level and using an electronic structure input file as the higher level may be used for variational transition state theory and any of the types of tunneling calculations.

Reaction paths may be calculated by the Euler steepest-descents, Euler stabilization, Page-McIver, or variational reaction path algorithms. Vibrations away from the reaction path may be defined by rectilinear, nonredundant curvilinear, or redundant curvilinear coordinates. Generalized-transition-state dividing surfaces may be defined on the basis of gradient directions or by the re-orientation of the dividing surface algorithm.

POLYRATE supports six options for direct dynamics, namely (i) straight single-level direct dynamics, (ii) zero-order interpolated variational transition state theory (IVTST-0), (iii) first-order interpolated variational transition state theory (IVTST-1), (iv) interpolated variational transition state theory by mapping (IVTST-M), (v) variational transition state theory with interpolated single-point energies (VTST-ISPE), and (vi) variational transition state theory with interpolated optimized corrections (VTST-IOC). VTST-IOC and VTST-ISPE are examples of dual-level direct dynamics; and VTST-IOC is also called triple-slash dynamics (///), where the triple slash denotes higher-order corrections of the geometries at which energetic and Hessian corrections are calculated. Dual-level methods may be applied with electronic structure data for both levels (dual-level direct dynamics), or it may be applied with an analytical potential energy surface for the lower level and electronic structure data for the higher level. When dual-level methods are employed with electronic structure data for both levels, the lower level may be either straight direct dynamics or IVTST-M.





 

QuanteMM combines quantum mechanics and molecular mechanics, allowing you to use accurate first-principles methods to study a reaction center while taking the surrounding environment fully into account. Large and complex systems like zeolite pores, enzyme active sites, and metal oxide surfaces can be studied with high accuracy. It is available from Accelrys.





 

Re_View is a Windows program that enables the visualization and analysis of dynamic reaction data such as conformational analysis, reaction pathways, vibrational modes, etc.





--- S, T, U ---





 

SCARECROW A program for the display of molecular structures and the analysis of molecular dynamics trajectories. SCARECROW will not be developed any further from the level it was at spring 1994. SCARECROW was originally written just for SGI machines using their graphics library (GL).

Now when OpenGL is available for almost all machines (hardware platforms) SCARECROW has been rewritten into gOpenMol. The program is a superset of the old implementation.. Contact:

Leif Laaksonen
Center for Scientific Computing
P.O. Box 405
FIN-02101 Espoo, FINLAND
Tel: +358-0-4572378
Fax: +358 0 4572302
E-mail: Leif.Laaksonen@csc.fi




 

SIgMA, is a system of programs and data files for running

  • Energy minimization
  • Free Molecular dynamics
  • Constrained and restrained molecular dynamics
  • Molecular dynamics with free-energy methods

of biological macromolecules. Using Sigma one can work with periodic boundary conditions and simulate molecules in solvent water. (In principle, Sigma can also handle the more complex periodicity of crystals. However, the currently running fast version of Sigma cannot handle any except orthogonal P1 "symmetry".)

The program was developed in Jan Hermans' lab, and is available at http://femto.med.unc.edu/software.html. The source code is free and it is available (with parallel version) for most UNIX and Linux flavors.





 

TINKER molecular modeling software is a complete package for molecular mechanics and dynamics of molecules, especially polypeptides. TINKER has the ability to use any of several common parameter sets, such as AMBER/OPLS, CHARMM22, MM2, MM3, AMBER-95, ENCAD, MMFF-94, MM4 (last 3 in progress) and our own TINKER set. It also implements a variety of novel algorithms such as: a new distance geometry metrization method that is much faster than standard algorithms, Elber's reaction path methods, modified versions of Scheraga's Straub's global optimization via potential smoothing, multipole expansion Macromodel GB/SA solvation, our own truncated Newton (TNCG) local optimizer, surface areas and volumes with derivatives, a simple free energy perturbation facility, normal mode analysis, minimization in torsional space, a new spherical energy cutoff method, reaction field treatment of long range electrostatics, and much more....

The distribution version of TINKER, with full source code, is made available free of charge to anyone who wants it. The distributed code is written in a clean, simple subset of Fortran77. A working f2c translated version in C is also provided. We do not and will not provide binaries, as it is expected that users will build the package on their local machines. The basic package has been used by the Ponder lab and others at Washington University since about 1991 and should be fairly robust. All we ask is that you notify us of any bugs, features you would like added, or major code extensions that you add youself. If you make significant use of the package, please return the enclosed license form.

Comments are welcome and should be sent via email to ponder@comet.wustl.edu. For additional information, contact:

Jay W. Ponder
Biochemistry, Box 8231
Washington University Medical School
660 South Euclid Avenue
St. Louis, Missouri 63110 USA
Phone: (314) 362-4195
Fax: (314) 362-7183
Email: ponder@comet.wustl.edu




--- V, W ---





There are currently no titles available in this section of the software listings.







--- X, Y, Z ---





 

ZMM-MVM is made up of two programs with ZMM as a modelling program and MVM as a display program. We are distributing both programs together. ZMM is a commercial software and MVM is a freeware for Molecular Visualization and Modeling.





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