121 projects tagged "Chemistry"

Download Website Updated 23 Dec 2003 KMovisto

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Pop 39.90
Vit 3.83

KMovisto is a free molecule viewer which reads GAUSSIAN files, exports POV-Ray scripts for high quality presentations, and VRML files for creating 3D molecule sceneries for the Web.

Download Website Updated 28 Oct 2011 NAMD

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Pop 63.80
Vit 9.19

NAMD is a parallel, object-oriented molecular dynamics program designed for high-performance simulation of large biomolecular systems.

Download Website Updated 16 Nov 2004 Viewmol

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Pop 50.48
Vit 2.51

Viewmol is a program for building and editing molecules as well as for the visualization of outputs from quantum chemical and molecular mechanics programs. Currently supported are Gaussian 9x, Gamess, Discover, DMol/DSolid/DMol3, Gulp, Mopac, Turbomole, and PDB files. Properties visualized include geometry (with various drawing modes), vibration (animated or with arrows), optimization history/MD trajectories, MO energy level diagram, MOs, basis functions, and electron density. Drawings can be saved as TIFF, HPGL, Postscript, and input files for Rayshade. Viewmol has an embedded Python interpreter for automation. The program is language independent and currently "speaks" English, French, German, Russian, or Spanish.

Download Website Updated 14 Feb 2012 VMD

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Pop 134.54
Vit 13.14

VMD (Visual Molecular Dynamics) is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. VMD uses OpenGL and OpenGL Programmable Shading Language for high performance rendering of large structures.

Download Website Updated 30 Nov 2005 XDrawChem

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Pop 122.51
Vit 9.51

XDrawChem is a program for drawing chemical structures. Features include fixed length and fixed angle drawing, a ring tool to automatically draw rings, automatic alignment of structures in reactions, 2D structure diagram generation, and 3D structure conversion. It can access structures in the PubChem compound database by name, CAS number, or formula. It can output InChI for structures and search the database by structure. It can predict 1H NMR, 13C NMR, simple IR spectra, and estimated pKa. XDrawChem can work with its native file format, ChemDraw files, and any format supported by OpenBabel (MDL Molfile, CML, etc.).

Download Website Updated 08 Mar 2001 Jude

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Pop 23.15
Vit 1.42

Jude is a rapid application development tool to develop data management workgroup applications that easy-to-maintain for developers and easy-to-use for end users. It is based on a knowledge base with an object oriented structure on the server side and a compound document agent-based user interface on the client side.

No download Website Updated 16 Mar 2006 CatDCD

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Pop 21.54
Vit 1.80

CatDCD functions much like the Unix "cat" command: it concatenates DCD files into a single DCD file. You can also use CatDCD to write only selected atoms to the final DCD file.

Download Website Updated 02 Mar 2001 FlipDCD

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Pop 16.06
Vit 1.00

FlipDCD is a small utility for reversing the endianism of binary DCD trajectory files from Charmm and NAMD. This can be useful when running simulations on one architecture and visualizing or analyzing the results on another. FixDCD is a tiny utility to modify the header of an X-PLOR DCD file to make it readable by programs expecting Charmm DCD files, at the expense of a Timestep size value in the header.

Download Website Updated 02 Mar 2001 MatDCD

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Pop 16.73
Vit 1.00

MatDCD is a Matlab package for reading/writing DCD-formatted molecular dynamics trajectory files. It supports Charmm and xplor-format DCD files, it can read both big- and little-endian storage formats, and it can specify which atom indices to load without having to load the entire file.

Download Website Updated 02 Mar 2001 Mindy

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Pop 17.20
Vit 1.00

Mindy is a very simple serial molecular dynamics program derived from NAMD source code. It currently uses xplor parameter and structure files. The program is written in very straightforward C++.

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openAviToGif

A video to GIF converter.

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libcap-ng

An alternate POSIX capabilities library.