Molecular Vibrations

This is set of functions that allow opening of Molecular Imaging atomic force microscope files into Matlab matrix. Unzip the files in one directory and type in Matlab command prompt:y=ReadSTP('pathfilename.stp',buffer number).Matrix y will contain z values of measured surface. Comments will show...

MDDriver is a library allowing a user to easily couple molecular visualisation tools with simulation code through a network. It allows to carry out interactive molecular dynamics, visualize simulation results and drive a simulation in interactive time.

The main program is Main_sound_and_vibs.m. Up to 100 metrics are for each of sound, hand arm vibrations, whole body vibrations, and motion sickness. Main_sound_and_vibs calls the primary depedent function"Continuous_Sound_and_Vibrations_Analysis" which contains the switch statement controlling...


Platforms: Matlab

This submission contains an implementation of the modal substructuring approach described in Chapter 9 of Ginsberg, d-deDUMechanical and Structural Vibrations,d-deDt Wiley, 2001. The well known Craig-Bampton component mode synthesis method is a special case of the approach implemented here. The...


Platforms: Matlab

this can be used to extract the frequency of a simple harmonic vibrations from framesvibration_from_images.m is a function that can be used to extract the frequency of a simple harmonic vertical vibration. The mass has to have a horizontal landmark.The included video (Video.avi) has been recorded...


Platforms: Matlab

analyzes different features of multiple primers simultaneously, the melting temperature calculation for standard and degenerate oligonucleotides, GC content, primer PCR efficiency; primers are analyzed for all primer secondary structures including G-quadruplexes detection, hairpins, self-dimers...


Platforms: Mac

OpenThermo is a program package for statistical thermodynamics computations beyond rigid rotor harmonic oscillator approximation (RRHOA), with taking into account internal rotations and vibration anharmonicity. Such calculations often require individual approach for every molecule, and their...


Platforms: *nix

MDAnalysis is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, or Amber. It allows one to read molecular dynamics trajectories and access the atomic coordinates through numpy arrays. This provides a flexible and relatively...


Platforms: Mac

Jamberoo (former JMolEditor) is a program for displaying, analyzing, editing, converting, and animating molecular systems. A program is in constant development to improve the existing code and to add new functionality.


Platforms: Mac

Sander is the AMBER module which carries out energy minimization, molecular dynamics, and NMR refinements. The acronym stands for Simulated Annealing with NMR-Derived Energy Restraints, but this module is used for a variety of simulations that have nothing to do with NMR refinement. Sander uses...


Platforms: Mac

Cryogenic instruments for both scientific and (earth) observation satellites have increasing demands in measurements accuracy. Low temperature station without any vibrations and without cryogenics liquid is now possible. See more information on our product leaflet here: ESU 20K & ESU 6K


Platforms: Mac

NCL is a C++ library for interpreting data files created according to the NEXUS file format used in molecular evolution and phylogenetic systematics.


Platforms: Mac

HOT is a package originally constructed for combustion modeling in Matlab. It calculates common thermodynamic properties such as enthalpy, specific heat, entropy, internal energy, gamma, ideal gas constant, molecular weight, etc


Platforms: Matlab

NanoVis (beta version) allows to visualize any atomistic structure by reading a user defined file. The supported formats are "gen" and "xyz". There are two display modes: normal and "spacefill". In the zip file, with the .m file, there are two examples of structure and a file containing the atoms...


Platforms: Matlab

This function allows calculating the compressibility factor, the coefficient of fugacity and density of a pure compound using the modified Iwai-Margerum-Lu Cubic Equation of State (IML-CEoS).The next data are necessary: temperature, pressure, molecular weight, acentric factor, and experimental...


Platforms: Matlab

The suite aims to help automatizing and batch processing the molecular docking studies of DNA-Drug complexes. All the upcoming programs work on Windows, Mac and Linux.


Platforms: Mac

The EJS Molecular Dynamics Demonstration model is constructed using the Lennard-Jones potential truncated at a distance of 3 molecular diameters. The motion of the molecules is governed by Newton's laws, approximated using the Verlet algorithm with the indicated Time step. For sufficiently small...


Platforms: Mac

The Molecular Dynamics Adiabatic Piston model shows two gas samples within a horizontal cylinder that is divided by an insulated piston that moves without friction. It is a supplemental simulation for an article by Eric Gislason "A close examination of the motion of an adiabatic piston" in the...


Platforms: Mac

Path-O-Gen is a tool for investigating the temporal signal and 'clocklikeness' of molecular phylogenies. It can read and analyse contemporaneous trees (where all sequences have been collected at the same time) and dated-tip trees (where sequences have been collected at different dates). It is...


Platforms: Mac

gMol is an interactive visualization system used to display and manipulate 3-dimensional models of scientific data, such as molecular structures and surfaces. It contains both OpenGL and web browser widgets that enable flexible user interfaces.


Platforms: *nix