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<!DOCTYPE html>
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<title>Linux4Chemistry (old posts, page 4) | Linux4Chemistry</title>
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<h1 class="title"><a href="posts/vasp.html">VASP</a></h1>
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<time class="timeago" datetime="2013-03-04T00:00:00+01:00">2013-03-04 00:00</time>
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<li><a class="tag p-category" href="categories/molecular-dynamics.html" rel="tag">Molecular Dynamics</a></li>
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<p>Package for performing ab-initio quantum-mechanical MD using pseudopotentials and a plane wave basis set. The approach implemented in VAMP/VASP is based on a finite-temperature local-density approximation (with the free energy as variational quantity) and an exact evaluation of the instantaneous electronic ground state at each MD-step using efficient matrix diagonalization schemes and an efficient Pulay mixing.</p>
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<h1 class="title"><a href="posts/vasp-data-viewer.html">VASP Data Viewer</a></h1>
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<time class="timeago" datetime="2013-03-04T00:00:00+01:00">2013-03-04 00:00</time>
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<p>VASP Data Viewer is a visualization program for examining output files generated by the quantum chemistry package VASP.</p>
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<h1 class="title"><a href="posts/vb2000.html">VB2000</a></h1>
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<time class="timeago" datetime="2013-03-04T00:00:00+01:00">2013-03-04 00:00</time>
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<p>VB2000 is an ab initio electronic structure package for performing modern Valence Bond (VB) calculations based on a highly efficient VB algorithm - the so called Algebrant Algorithm. It has also a general implementation of the Group Function (GF) Theory, in which a large molecule is described in terms of its constituent parts of physically identifiable "electron groups". It can be used as a stand-alone program, or as a plug-in module for GAMESS and Gaussian.</p>
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<h1 class="title"><a href="posts/vega.html">VEGA</a></h1>
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<time class="timeago" datetime="2013-03-04T00:00:00+01:00">2013-03-04 00:00</time>
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<li><a class="tag p-category" href="categories/gpl-compatible.html" rel="tag">Gpl Compatible</a></li>
<li><a class="tag p-category" href="categories/molecular-dynamics.html" rel="tag">Molecular Dynamics</a></li>
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<p>VEGA was developed to create a bridge between most of the molecular software packages, like BioDock, Quanta/CHARMm, Insight II, MoPac, etc. In this tool have been also implemented some features that are useful to analyze, display and manage the 3D structures of molecules.</p>
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<h1 class="title"><a href="posts/vibrate.html">Vibrate</a></h1>
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<p>Vibrate is a program for visualizing the normal vibrational modes of a molecule. Vibrate can read files generated by Mopac, Gaussian (G92 and G94), and HONDO and display the computed vibrational spectrum.</p>
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<h1 class="title"><a href="posts/viewmol.html">Viewmol</a></h1>
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<p>Viewmol is an open source graphical front end for computational chemistry programs. It can be used to build molecules, trace a geometry optimisation or MD trajectory, show vibrations, draw IR or Raman spectra, MO energy diagrams, and much more.</p>
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<h1 class="title"><a href="posts/vmd.html">VMD</a></h1>
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<time class="timeago" datetime="2013-03-04T00:00:00+01:00">2013-03-04 00:00</time>
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<p>VMD is a program for visualization and analysis of the results of computational chemistry and molecular dynamics calculations. It can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation.</p>
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<h1 class="title"><a href="posts/volsurf.html">VolSurf</a></h1>
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<p>VolSurf is a computational procedure to produce 2D molecular descriptors from 3D molecular interaction energy grid maps. The basic idea of VolSurf is to compress the information present in 3D maps into a few 2D numerical descriptors which are very simple to understand and to interpret.</p>
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<h1 class="title"><a href="posts/wat2ions.html">Wat2ions</a></h1>
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<time class="timeago" datetime="2013-03-04T00:00:00+01:00">2013-03-04 00:00</time>
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<p>Wat2ions uses the electrostatic potential map pre-computed by DelPhi to replace a certain number of the water molecules of the bath, surrounding a solvated macromolecule, with ions. The new coordinates are output to a PDB file.</p>
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<h1 class="title"><a href="posts/webmo.html">WebMO</a></h1>
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<time class="timeago" datetime="2013-03-04T00:00:00+01:00">2013-03-04 00:00</time>
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<p>WebMO is a WWW-based interface to Gamess, Gausssian, Molpro, Mopac, Nwchem, Qchem, and Tinker for setting up, submitting, and visualizing results of computational chemistry jobs.</p>
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