Graphic Apps    CAD     gOpenMol

gOpenMol 3.00


Description of

gOpenMol


gOpenMol is a software for the visualization and analysis of molecular structures and their chemical properties. The software uses Tcl/Tk scripting engine and can thus be easily extended without modifying the kernel code. gOpenMol can also be extended by writing extensions using sharable objects (Linux/Unix) and dynamic data exchange (Windows) modules. Moreover there is a set of programs and utility functions included in gOpenMol.gOpenMol has its background in the SCARECROW program, which was introduced at the beginning of the 90s. In the middle of the 90s prof. Geerd Diercksen asked for a graphical interface for his OpenMol set of programs. This triggered off the development of gOpenMol.1. gOpenMol can be used for the display and analysis of2. molecular structures and properties calculated with external programs,3. molecular dynamics trajectories,4. isocontour surfaces of grid data, such as molecular orbitals and electron densities.5. cut planes through grid data sets, and it can also be used to make short animations where a cut plane travels through a molecule grid data.6. The software can also be used together with electrostatic potentials from programs like GaussianXX, GAMESS Jaguar, UHBD (University of Houston Brownian Dynamics), AutoDock and the GRID programs.gOpenMol can be understood as two applications talking to each other through the command line interpreter:1. the kernel part containing the C-coding and the graphics (OpenGL) part2. and the Tcl/Tk based GUI.These two parts talk to each other through the command line interpreter located in the kernel part. When an option is selected from the GUI the equivalent line command is generated and sent to the interpreter. This is a very convenient and simple procedure. However, the opposite is not that easy. The kernel can of course talk with the GUI but it is more complicated and needs a bit more coding and I haven't been able to create a neat and handy way to do that.gOpenMol is hopefully a multipurpose analysis program. Currently the software has all of the molecular dynamics analysis features of the old SCARECROW and a lot of new features. Currently gOpenMol supports a wide range of molecular coordinate input formats:1. ADF, Amsterdam Density Functional output log files. If file contains multiple coordinates the coordinates will be merged to a multi-coordinate set XMOL file to be displayed using the trajectory analysis tools.2. CHARMm/CHARMM.3. CML file format.4. Chem3D binary file (plugin must be enabled).5. DL_Poly CONFIG coordinate file format.6. A frame from a trajectory (please look at the supported trajectory formats).7. Gaussian formatted checkpoint file.8. Gromos96 coordinate file format.9. Gromacs coordinate file format.10. HyperChem.11. Insight (car files).12. Jaguar coordinates from a Jaguar output log file.13. Mol2.14. Mumod.15. OpenMol (center binary file).16. PDB (Brookhaven Protein Data Bank format).17. Tinker coordinate file.Spartan binary file (plugin must be enabled).1. University of Houston Brownian Dynamics (UHBD) close to PDB format.2. Xmol single and multi xyz coordinate set file.3. XYZ general xyz coordinate file.4. YASP.gOpenMol supports several binary trajectory formats. Those formats marked with a "*" should be readable by gOpenMol independent of the hardware platform on which they have been created. This means that these trajectory files can be moved from one platform to an other without the need conversion. Supported file formats include:1. Amber*. Program included for the unformatting of formatted AMBER trajectories.2. Cerius2*3. CHARMm*/CHARMM*. Program included for the formatting/unformatting of CHARMm/CHARMM trajectories.4. Discover5. DL_Poly6. GROMOS* (Supporting the old GROMOS format)7. GROMACS* (trn, trr and xtc formats)8. HyperChem (I haven't tested with the latest version)9. MUMOD *10. XPLOR*11. YASP*and the following ascii trajectory formats:1. Amber formatted trajectory format.2. DL_Poly trajectory format.3. GROMOS96 trajectory format.4. TINKER multi frame coordinate trajectory format.5. XMOL xyz multi-step data sets. The included Xvibs software enables the display of vibrational modes from the GAUSSIANXX and GAMESS programs.Run the installation script install with the command: ./installYou are now ready to use gOpenMol. To run gOpenMol write: bin/rungOpenMolUninstall gOpenMolBoth the Unix and the Windows versions can be removed by just deleting the root directory and the directories under the root.


Published by: csc.fi
Downloads: 626
File Size: 26.6 MB
License: Freeware
Product Homepage: Visit csc.fi
Release Date: 08 October, 2012
OS: Windows
Download Location: Primary Download Link Broken? Report it!


gOpenMol 3.00 Download Tags:


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