LinuxLinks.com
Newbies What Next ? News Forums Calendar
Home | Register | News | Forums | Portal Pages | MyLinks | New | Hot | Link Us

Search/Browse

 Category Gateway
More Options
Category:  


LinuxLinks News
 · Nifty Free Image Viewers
 · Compact Text Editors Great for Remote Editing and Much More
 · Excellent Subtitle Editors
 · Small Console Menu Utilities
 · Make Downloading Files Effortless
 · Free Office Suites that Cut The Mustard
 · Low-Spec Hardware? Try these Desktop Environments
 · Powerful Command-line File Transfer Programs
 · Great Apps to Take Notes
 · Exciting New Terminal Emulators
(more...)

 

Latest Links
jdkdrum
lolcat
(more...)

 



Top : Software : Scientific : Chemistry : Molecular Dynamics

Highlights
Nifty Free Image Viewers
One of my favorite adages is "A picture is worth a thousand words". It refers to the notion that a still image can convey a complex idea. Images can portray a lot of information quickly and more efficiently than text. They capture memories, and never let you forget something you want to remember, and refresh it in your memory.

(Read more)
CAM Expert
(commercial) A professional CAD/CAM system for engraving, LASER cutting and many other uses.

Links:

  • Almond
    (commercial) Almond is specifically developed for generating and handling alignment independent descriptors called GRIND (GRid INdependent Descriptors). These are a new generation of 3D-molecular descriptors with application in 3D-QSAR, QSAR, virtual screening, design of combinatorial libraries, selectivity studies and in any field where 3D quantitative pharmacophoric description for (macro)molecules is needed.
  • AmberFFC
    AmberFFC is designed to convert six AMBER force fields (FF) (Amber 91, Amber 91X, Amber 94, Amber 96, Amber 98 and Amber 99) freely available in the public domain.
  • B-BOP
    B-BOP (a program package for Block Bond-Order Potential method) is a program package for performing O($N$) tight-binding (TB) calculations of molecules and bulks, based on block bond-order potential method within semi-empirical TB models.
  • FTrees
    FTrees is a highly efficient software tool for fuzzy similarity searching facilitating virtual HTS. The ability to detect novel molecular scaffolds is one of several features that charaterizes FTrees capabilities.
  • GROMACS
    GROMACS is a versatile package for performing molecular dynamics. Features include: standard MD simulations, energy minimizations, NMR refinement using NOE data, high performance due to well optimized code and smart algorithms, automatic topology generation from a building block library, flexible force field usage, non-equilibrium MD, many analysis and preprocessing tools. Read more
  • HONDOPLUS
    HONDOPLUS is a version of HONDO 99.6 with additional modules for evaluating Lwdin and CM2 partial atomic charges and for carrying out SM5.42R continuum solvation calculations by Hartree-Fock and hybrid DFT-Hartree-Fock methods.
  • LAMMPS
    LAMMPS is classical molecular dynamics (MD) code created for simulating molecular and atomic systems such as proteins in solution, liquid-crystals, polymers, zeolites, or simple Lenard-Jonesium. It was designed for distributed-memory parallel computers and runs on any parallel platform that supports the MPI message-passing library or on single-processor desktops or laptops.
  • MacroModel
    (commercial) MacroModel allows the graphical construction of complex chemical structures and the application of molecular mechanics and dynamics techniques in vacuo or in solution.
  • MDTools
    MDTools is a Python module which provides a set of classes useful for the analysis and modification of protein structures. Current capabilities include reading psf files, reading and writing (X-PLOR style) pdb and dcd files, calculating phi-psi angles and other properties for arbitrary selections of residues, and parsing output from NAMD into an easy-to-manipulate data object.
  • MOLMOL
    MOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR.
  • MOSCITO
    Moscito is designed for condensed phase and gas phase MD simulations of molecular aggregates. Standard molecular mechanics force-fields such as AMBER, OPLS, CHARMM and GROMOS can be employed. Simulations can be carried out in different ensembles such as NVE, NVT or NPT using the weak coupling scheme. (Smooth Particle Mesh) Ewald summation is used for long range electrostatic interactions. Read more
  • Music
    Music (Multi-purpose SImulation Code) is an object-oriented package intended to perform various types of Molecular Dynamics and Monte Carlo simulations with user-specified forcefields. It can be used to simulate diffusion and adsoprtion in zeolites, for liquid and gas simulations as well, and may be easily extended for solid simulations.
  • NAB
    NAB was originally designed as a small modeling language (a "molecular awk"), with a principal focus on constructing models for non-helical nucleic acids. It has been used to construct models of helical and non-helical nucleic acids from a few dozen to a few hundred nucleotides in size, and provides a combination of rigid body transformations and distance geometry to create candidate structures that match input criteria. We have applied NAB to duplex-, triplex- and tetraplex DNA, to RNA hairpins and pseudo-knots, to closed-circular DNA, and to models of the small subunit of the ribosome and of recombination sites.
  • nMOLDYN
    nMOLDYN is an interactive analysis program for Molecular Dynamics simulations. It is especially designed for the computation and decomposition of neutron scattering spectra, but also computes other quantities.
  • Packmol
    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.
  • PINY_MD
    PINY_MD(c) is a multipurpose, object-oriented molecular simulation package developed as a collaborative effort between Indiana University, New York University and the University of Pennsylvania. PINY_MD(c) is capable of performing a wide variety of molecular dynamics, electronic structure, and geometry optimization calculations.
  • PyVib2
    PyVib2 permits the automatic correlation of vibrational motions of molecules, thereby allowing an understanding of Raman, Raman optical activity (ROA), infrared vibrational absorption (IR), and vibrational circular dichroism (VCD) spectra. The versatile representation of vibrational motions, the visualization techniques of Raman/ROA and IR/VCD generation in molecules, and the production of publication quality spectra are features of PyVib2.
  • RM1
    RM1 is a natural extension to AM1 and PM3 (PM5 and PM6 use different equations, which mainly affect the way the core-core interaction is defined); capable of modeling most molecular systems of importance to organic chemistry, biochemistry and pharmaceutical research; a new, recently developed, fully disclosed, and public domain semiempirical molecular orbital model.
  • Simulaid
    SIMULAID is a collection of utilities designed to help setting up molecular simulations.
  • Tinker
    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 and ff99), CHARMM (19 and 27), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA and OPLS-AA/L), Liam Dang's polarizable potentials, and our own AMOEBA polarizable atomic multipole force field. Parameter sets for other standard force fields such as GROMOS, UFF, ENCAD and MM4 are under consideration for future releases.
  • VEGA ZZ
    VEGA was developed to create a bridge between most of the molecular software packages, like BioDock, Quanta/CHARMm, Insight II, MoPac, etc.
  • ZMM
    (commercial) ZMM is a molecular modeling program for theoretical studies of systems of any complexity: small molecules, peptides, proteins, nucleic acids, and ligand-receptor complexes.



Share this Page
Bookmark and Share
Submit this page to popular social networks such as Digg, Twitter, StumbleUpon and more.


My LinuxLinks
MyLinks
  • Bookmarked links
  • Emailed Newsletter
  • Your own profile

  • Top Applications
    Top Free Software
    6 Lean Desktops
    14 File Managers
    21 Backup Tools
    21 Window Managers
    21 Productivity Tools
    21 Text Editors
    21 Video Emulators
    21 Home Emulators
    42 Graphics Apps
    42 Scientific Apps
    42 Email Apps
    12 Instant Messaging
    42 Games
    42 More Games
    21 More Games
    42 Audio Apps
    42 Video Apps
    80 Security Apps
    Free Console Apps
    14 Multimedia
    'Free' Proprietary
    21 Closed-Source Apps
    Top Commercial Apps
    42 Games
    Free Web Software
    21 Web CMS
    14 Wiki Engines
    8 Blog Apps
    6 eCommerce Apps
    Other Articles
    Migrating from Windows
    Distribution Guide
    Distro Portal Pages

    Migrate to Linux
    Thinking of switching to Linux? Check out our Linux Equivalents to Windows Software section, highlighting popular Linux equivalents to Windows software.

    This feature also includes over 150 individual software portal pages including Blender, Scribus, OpenOffice.org, Evolution, Eclipse, K3b, and MythTV, providing a wealth of essential information.

     

    Distribution Guides
    Distro Guide

    Debian
    Fedora
    Gentoo
    Mandriva
    OpenSuSE
    RedHat
    Slackware
    Ubuntu
    Xandros

    Absolute
    Linux Mint
    64 Studio

    LiveCDs
    Berry Linux
    GoblinX
    KNOPPIX
    Kubuntu
    NimbleX
    PCLinuxOS
    Sabayon
    SimplyMEPIS
    Xubuntu

    Entire List

     

    Services
    Web Calendar
    Linux Licenses

    Advertise at LinuxLinks.com

     

    Latest Portal Pages
    Mixxx
    energyXT2
    GRASS
    uDig
    QGIS
    gretl
    SPSS

     

    Add Link | Modify Link | About | FAQ | Guide | Privacy | Awards | Contact | SourceFiles.org
    Portal Version 0.7. Intel Blade.
    Comments to the webmaster are welcome.
    Copyright 2009 LinuxLinks.com All rights reserved.