Software Updates:
- Cambridge Software Database has a new graphical interface, Conquest, in
addition to quest, pluto, prequest, and vista. To use Conquest,
first you need to log into model0.ps.uci.edu, then, type:
>cq
- GaussView (GUI for the Gaussian software) is installed.
The command to call GaussView:
>gv
- Jaguar is a new software for ab initio calculations installed
in the modeling facility. To start this program:
>jaguar &
When you submit jobs, make sure to choose the right job
host under the run option of the main graphical interface.
- MacroModel is updated to version 7.0 from 6.5. There
is a new graphical interface called "maestro". Schrodinger Inc. will discontinue
developing older graphical interface although the modeling facility will keep
these GUI versions. Please familiarize yourself with maestro.
Commands to use MacroModel version 6.5:
>macromodel
To use MacroModel version 7.0:
>macromodel70
To call a new graphical interface:
>maestro
- NWChem is another software for quantum mechanical calculations.
In order to use this program:
>nice +10 nwchem input_filename > & output_filename
&
Example input files are available at /apps/nwchem/examples.
There are various molecular graphics programs for biological
molecules in the modeling facility. Manuals for most of these software are available
and they are placed in the bookshelf of the modeling facility.
>grasp
- Rater3D is also available.
- The command to call Jmol, a Java based molecule viewer
and editor:
>jmol
- In order to use the VMD program:
>vmd
- To use The Persistence of Vision Raytracer(POVray), a
high-quality tool for creating stunning three-dimensional graphics:
>povray +H500 +W401 -Iinput_file.pov -ooutput_file.tga
You can vary numbers after +H and +W according to your
need.