Introduction to gOpenMol


gOpenMol started as the graphical interface to the OpenMol set of programs but is today an independent toolbox for the display and analysis of results from a wide range of computational chemistry programs.

gOpenMol features include:

Software:

gOpenMol can import, display and analyze several different input coordinate file formats and binary trajectory file formats. The program has a graphical user interface (GUI) and an internal line command interpreter based on the Tcl/Tk interpreter. More details about the Tcl/Tk scripting language can be found at the address:

http://dev.scriptics.com

gOpenMol can be used for a wide range of analysis and display tasks like the display of isocontour surfaces and cross sections of grid data.

Hardware:

gOpenMol graphics is implemened using the OpenGL (http://www.opengl.org) or MESA (http://www.mesa3d.org) graphics libraries. Using the MESA graphics library it is possible to turn gOpenMol into pure X-Windows application, where no extra graphics hardware is needed.

gOpenMol is currently supported on two promary hardware platforms:

However gOpenMol has been running on the following platforms during the develoment phases.

gOpenMol should run on any Unix platform without any changes.

Possibilities:

gOpenMol is hopefully a multipurpose program. Currently the program has most of the molecular dynamics analysis features of SCARECROW and a lot of new features. Currently gOpenMol supports a wide range of molecular coordinate input formats:

gOpenMol supports the following binary trajectory formats:

and the following ascii trajectory format:

Extensive display isocontour surfaces and cut planes for:

Utility programs

All these executable programs are located in the bin/ directory and the source code is in the utility/ directory.

ambera2b
Converts a formatted ascii AMBER trajectory into a unformatted one. gOpenMol can only handle unformatted AMBER trajectories.
charmmtrj
This program makes the formatted/binary tranformation for a CHARMM dynamics trajectory file.
contman
Performs a variety of operations on a contour (plt) file.
convert
Converts the output search results (FDAT) from Cambridge Structural Database into separate PDB files.
gcube2plt
Converts a cube file from the GaussianXX program into a binary format known by gOpenMol.
gridasc2plt
Converts a UHBD formatted PHI grid file into the plt format used by the gOpenMol progra,
gridbin2plt
Converts a UHBD unformatted PHI grid file into the plt format used by gOpenMol.
pltfile
This program can be used to format a binary plot file or to make a formatted file into binary. This program is helpful if you want to move the plot file from one computer hardware to an other.
sybyl2amber
Converts a formatted ascii Sybyl trajectory into an unformatted AMBER one.
trajmerge
Merges two CHARMM trajectory files into one.
xplor2charmm
Converts an XPLOR trajectory into a CHARMM trajectory.