Description

From the IQmol web site: IQmol is a free open-source molecular editor and visualization package. It offers a range of features including a molecular editor, surface generation (orbitals and densities) and animations (vibrational modes and reaction pathways).

• IQmol Home Page

Version

• 2.2

Authorized Users

• CIRCE account holders
• RRA account holders
• SC account holders

Platforms

• CIRCE cluster
• RRA cluster
• SC cluster

Running IQmol on CIRCE

Modules

IQmol requires the following module file to run:

• apps/iqmol/2.2

• See Modules for more information.

Starting the Application

First, you will need to have properly configured an X11 session. This can be accomplished using an “ssh -Y” connection from a Linux box or an SSH client in Windows. Alternatively, a CIRCE Desktop Environment session can also be used. For more information about the CIRCE Desktop Environment, please see our CIRCE Desktop Environment documentation.

Below is an example for using an ssh connection from the command line.

[user@localhost ~]$ ssh -Y circe.rc.usf.edu
[user@circe ~]$ module add apps/iqmol/2.2
[user@circe ~]$ iqmol

Finally, go to File->Open and open your molecule file.

Manuals and Test Data

• Official IQmol Documentation
  • http://iqmol.org/documentation.php
• Known IQmol sample inputs
  • /apps/iqmol/2.2/samples

Reporting Bugs

Report bugs with IQmol to the IT Help Desk: rc-help@usf.edu