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Top : Software : Scientific : Chemistry : Molecular Dynamics

5 Highly Promising Terminal Emulators
The terminal emulator is a venerable but essential tool for computer users. The reason why Linux offers so much power is due to the command line. The Linux shell can do so much, and this power can be accessed on the desktop by using a terminal emulator. There are so many available for Linux that the choice is bewildering.

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  • 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 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 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 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 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 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 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(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.
  • 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.

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