Practical Information on Using Gaussian 98

On the Gustavus Computational Server

Gaussian 98

http://www.gaussian.com/

 Gaussview: front-end to Gaussian 98

Gaussview is an X-windows based molecular visualization program particularly well-suited to submitting calculations to Gaussian 98 and examining these results.  Gaussian 98 is a comprehensive and state of the art quantum mechanical computational package.  The Gaussview program and Gaussian package run on Slater, our dual Pentium computational server, under Linux.  When running the program at the Slater console, simply type gv instead of xgv in an xterm window.  This will initiate Gaussview with higher quality Open GL graphics.  These programs will often be run remotely through an X-client.  On Windows machines we will run an X-client known as Exceed.  On other UNIX machines running X-windows the X-client is straightforward to initiate.  The specifics of initiating this program on an X-client are given below.

 

 Exceed

1) Make sure Exceed is running. Under Start menu find Exceed and then find Exceed from the many possibilities and start it.

2) Find Teraterm SSH and start this program. It may be under Internet or just on Start menu.

3) Log into slater.chem.gac.edu using pchem username.

4) Initiate Gaussview.

To initiate Gaussview type:

 xgv {-display ip address:0}  &

this should be optional: where ip address is the ip adress of the machine you are working on.  Gaussview will start in a panning mode.  If you don't care for this mode right-click on window title line and maximize. When finished exit Gaussview

Note: if you open a file that does not include a final geometry Gaussview will lock-up.  If this happens, click on x to close window and use up arrow in TeraTerm window to get last command to restart Gaussview.

 Printing

Within Gaussview use print from the file menu to create an encapsulated postscript file.  Give this file a .eps file ending.  This file is saved in your directory to be printed with the use of a couple of other commands (note: print command does not actually print).  The encapsulated postscript file must first be converted to a postscript file using the convert command (type man convert at the command prompt to learn about the convert program). 

·        Type convert -page Letter eps filename ps filename

·        To print type lpr -Pvisualize ps filename

·        To check print queue type lpq -Pvisualize

 Editing Files

·        Connect to Slater (see above under Exceed)

·        To initiate Xemacs type:

xemacs {-display ip address:0}  &

xemacs is a very versatile text editor under Linux.

 

xemacs Website: XEmacs: The next generation of Emacs

Editing commands are as given on "Reference Card"

Submitting Calculations to Gaussian 98

·        Create Input deck with Gaussview or Xemacs (text editor) or a combination.

·        Use command g98_submit  job-name & at the command line prompt.

Working in UNIX

Useful commands: (type at Telnet command line)

ls	list files in current directory
ls -l	list files with date, size information
cp  file1  file2	copy file1 to file2
cd  directory	change directory to directory
cd ~	change directory to home directory
rm  file	remove file
"up arrow"	recall last typed line
&	background processing of preceding command
grep word file	find word in file and display every line with word in it.
cat file	Lists a file
More file	Lists a file by page
du	Disk usage
df -h -a	Provides information about disk space

 Scaling Factors for vibrational frequencies

Model Chemistry	Frequency scaling
HF/6-31G(d)	0.8929
B3LYP/6-31G(d)	0.9613

 

.com	Gaussian 98 input file (z-matrix)	zmat
.pdb	Protein data bank	pdb
.ent	Protein data bank	ent
.bgf	Biograf	bgf
.xyz	Unadorned cartesian	zyz
.inp	MOPAC	mopac
.cac	Cache	cache