Hints for Using Jaguar v. 4.2

Shusterman Research Group

This page is a compilation of hints and tricks for using Jaguar (www.schrodinger.com).

Alan Shusterman, March 2004

How do I optimize a molecule's geometry in "water"? (Mar 9, 2004)

Put isolv=2 and nogas=2 in the &gen section. (The second keyword prevents gas phase pre-opt of geometry).
 

How do I optimize a geometry in Cartesian coordinates? (Mar 9, 2004)

Put intopt=0 in the &gen section.
 

How do I start the Jaguar GUI (without using Maestro)? (Feb 2, 2004)

Type jaguar gui in any Xwindow. Note: the current path to Jaguar is /usr/local/bin/jaguar.
 

How do I run a Jaguar calculation from the command line (without using the GUI?) (Feb 2, 2004)

Suppose your Jaguar input file is called nifty.in. Simply manuever to the same directory as this file and type jaguar run nifty.
 

How do I setup and run multiple Jaguar calculations from the command line? (Feb 2, 04)

If the jobs are located in the same directory:

1. Name input files: modelA.in, modelB.in, ...
2. Create Jobs.bat file in this same directory
3. Put input filenames in Jobs.bat, one name per line and without the suffix, e.g.,
 
modelA
modelB
 
4. Type jaguar batch Jobs from command line (working directory is same directory as Jobs.bat)

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If the jobs are located in different directories:
 
1. as above
2. Create Jobs.bat file in a suitable working directory, e.g., parent directory of job directories
3. Interleave pathnames and input filenames in Jobs.bat, e.g.,
 
WORKDIR=modelA
modelA
WORKDIR=modelB
modelB
 
4. Type jaguar batch Jobs from command line (working directory is same directory as Jobs.bat)