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: 646
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:


Files32.com collects software information directly from original developers using software submission form. Sometimes it can happen that software data are not complete or are outdated. You should confirm all information before relying on it. Using crack, serial number, registration code, keygen and other warez or nulled soft is illegal (even downloading from torrent network) and could be considered as theft in your area. Files32 does not provide download link from Rapidshare, Yousendit, Mediafire, Filefactory and other Free file hosting service also. The software has been submitted by its publisher directly, not obtained from any Peer to Peer file sharing applications such as Shareaza, Limewire, Kazaa, Imesh, BearShare, Overnet, Morpheus, eDonkey, eMule, Ares, BitTorrent Azureus etc..
gOpenMol Related Software

Qmol 4.02
Qmol is a OpenGL based molecular viewer. Qmol is a software for viewing molecular structures and animating molecular trajectories.

License:  Freeware
Platform:  Windows
File Size: 343.2 KB

 

RobotVisionCAD 1.0
RobotVisionCAD is a computer aided design for Image Processing and Computer Vision. RobotVisionCAD or in short RvCAD is a computer aided design for Image Processing and Computer Vision.

License:  Freeware
Platform: 
File Size: 5.3 MB

 

WorkXPlore 3D 1.6.4.0
A strong, full featured, high-speed CAD file viewer and analyzer. WorkXPlore 3D is distinguished by having a strong combination of full feature abilities, highest overall functionality, and...

License:  Shareware
Platform: 
File Size: 68.2 MB

 
 
Top Software

FTP Rush 2.1.8
FTP Rush is a free comprehensive FTP client for smooth file transfer. The program offers fully-fledged functionality delivered in a user-friendly interface and allows experienced users to create...

Crypt4Free by

Crypt4Free 5.47
Crypt4Free is files encryption software with ability to encrypt files and text messages. Support for ZIP files and ability to secure delete sensitive files. Skinnable user friendly interface.

Luxand Blink! by

Luxand Blink! 2.0
Login to your PC without touching a thing! Luxand Blink! is a free tool to let you log in to your Windows account by simply looking into a webcam - no passwords to type and no fingers to scan.

InTask Personal by

InTask Personal 1.5
InTask designed to help team leaders, developers and QA persons to share their efforts and deliver the products on time. The product includes fast task management, interactive gantt, document...

Pop-up Free by

Pop-up Free 1.56
Get rid of annoying popup windows and enhance your Web surf experience. Kill unexpected popup windows and protect your privacy. No more annoying advertisement windows and save your time.

Glary Utilities Portable by

Glary Utilities Portable 2.56.0.8322
One Click A Day For PC Maintenance, Keeps Any PC Problems Away. With 7 million worldwide users, the first-rank & free Glary Utilities is an INDISPENSABLE friend for your PC, with its 100% safe,...

VPSpro by

VPSpro 3.695
VPSpro is the ultimate in the creation of financial projection and general business plans. The unique walk-through process is simple to use and makes easy work of the hard parts of business planning.

Rylstim Budget Lite by

Rylstim Budget Lite 4.5.1.6376
Plan and manage your finances with a simple friendly calendar. Perfect solution for home users and freelancers!

Neox Screen by

Neox Screen 1.0.0.277
Neox Screen is a free application which with the help of the hotkeys you can take screenshots that are crystal sharp, small in size and ready to be shared.

EMCO Remote Installer Free by

EMCO Remote Installer Free 4.1.1
This free remote software deployment tool is designed to install and uninstall Windows software on remote PCs through local networks. You can use it to install and uninstall EXE setups and MSI...

Latest Software

DVDFab UHD Creator by

DVDFab UHD Creator 10.2.1.4
DVDFab UHD creator can produce premium 4K Ultra HD Blu-ray movies, using 4K H.265 MKV videos with HDR10 or Dolby Vision contents. The created 4K Blu-rays are of the studio-level specifications and...

ThesesAssistDrawer by

ThesesAssistDrawer 4.1.1
ThesesAssistDrawer is a small, yet powerful tool to assist the editing of theses, reports, or books. This program is compatible with 2007 or newer version of Microsoft Word.

Mapi for Gmail® 3.0
With Mapi for Gmail, Gmail becomes your default email client: Just right-click a file or select the 'Send by email' feature from any software and Gmail will open in a new message with the document...

PrecisionID OCR A and OCR B Fonts 2018
PrecisionID OCR-A and OCR-B Fonts include both upper and lower case letters as well as numbers, and several special characters and are designed for printing bank checks, passports, credit card...

HelpSmith by

HelpSmith 7.4.0.904
HelpSmith is the help authoring tool with Dynamic Styles support for creating CHM files, Web Help, PDF, and Printed Manual Documentation.

Nonlinear analysis - DataFitting by

Nonlinear analysis - DataFitting 1.7.29
DataFitting is a powerful statistical analysis program that performs linear and nonlinear regression analysis (i.e. curve fitting).

Magic Lines 4.0
An engaging and cute variation of the beloved Lines game with nice 3D effects! 3 balls per turn are placed on the playing board randomly. You need to line them up by color, and if you get 5 they...

IGES Viewer alias ABViewer by

IGES Viewer alias ABViewer 14
IGES Viewer is a professional software to work with 3D files. It supports IGS/IGES, STP/STEP, STL, OBJ, SAT, BREP, DWG, DXF, etc. The software has a dynamic 3D section tool, measuring tools and...

A VIP Simple To Do List by

A VIP Simple To Do List 2.9.58
VIP Simple To Do List is an easy tool for planning of your daily life. The program lets everyone who wants to stop wasting time and bring life in order quickly manage everyday tasks with help of...

Comodo Dragon by

Comodo Dragon 67.0.3396.99
Enjoy a faster, more stable and safer internet with Comodo Dragon. Dragon has the look and feel of Chrome with several security and functionality upgrades. Superior security and privacy, fast and...

User Time Control by

User Time Control 6.1.2.5
User Time Control Center lets you specify when exactly and how long the computer can be used. Schedule time intervals and the number of hours each child can use the computer per day a week.

VShell Server for UNIX 4.4
VShell SSH server is a secure alternative to Telnet and FTP on Windows, Mac, and UNIX providing strong encryption, robust authentication and data integrity. Fine-tune your environment with...

Related Searches

Currently Searching

Currently Downloading

JExplorer by

JExplorer 3.1
Java library, integrating Microsoft IE into Java apps as Java Swing UI component in headless mode, providing access to DOM, Explorer functionality, browser events, cookie management, proxy...

EditPlus by

EditPlus 2.31
EditPlus is an Internet-ready 32-bit Text editor, HTML editor and Programmer's editor for Windows. While it can serve as a good replacement for Notepad, it also offers many powerful features for...

Surpriise by

Surpriise 1.3
Surpriise is a joke program, incredible desktop entertainment, which brings a lot of fun to your kids, and the entire family or friends. This cute absolutely free program is a little gift for you,...

ANVSOFT 3GP Photo Slideshow by

ANVSOFT 3GP Photo Slideshow 1.12
3GP Photo Slideshow allows you to create entertaining 3GP MP4 format photo slideshows playable on 3GP compatible cellular phones.. With 3GP Photo Slideshow, you can quickly and easily produce...

xp style icons by

xp style icons Free
Unique XP style icons that come with highly professional designs for use in your applications. Each icon is available in four different sizes that includes 16x16, 24x24, 32x32 and 48x48. Each icon...

MPG Savings Calculator by

MPG Savings Calculator 1.01
This MPG Savings calculator will show you how much money you can save by getting better gas mileage on your vehicle.

Xinfire DVD Player by

Xinfire DVD Player 5.5.0.0
Xinfire DVD Player is a powerful region free DVD player & recorder, supporting to play multi Region DVD Movies without Region Code limit; delivering theatre-like movie watching experience with...

Norton Antivirus Definition Updates 7/22/2012
Norton AntiVirus is the world's leading anti-virus software. Just install it and forget it! it's always working in the background to protect your PC, and automatically updates its virus definitions...

SuperEZ Video Converter Free by

SuperEZ Video Converter Free 7.3.4
A one-for-all solution to convert video files of MPEG, AVI, MP4, SWF, FLV, WMV, RMVB, ASF, MOV, 3GP, etc. into MP3, WAV, WMA, OGG AAC, M4A, FLAC and MP2 files. The program provides all commonly...

TIFF into PDF by

TIFF into PDF 2.8.0.4
TIFF into PDF Converter utility software tool Supports Multi-page tiff file to PDF conversion, merge combine a number of multipage TIFs files to PDF.

Server Nanny Network Monitor by

Server Nanny Network Monitor 4.0.0
Reduce downtime and be the first to know when a server or network device fails by using Server Nanny network and server monitoring software.

The last time you had a network or server...

Animated Chart by

Animated Chart 2.2.1
Flash charts made easy. Software for generating animated interactive Flash charts and graphs for publishing to websites. Making graphs with Animated Chart is simple and quick and doesn't require...