[gmx-users] a query about analysis

[Mark Abraham]

----- Original Message -----
From: oguz gurbulak <gurbulakoguz at yahoo.com>
Date: Friday, June 18, 2010 21:36
Subject: [gmx-users] a query about analysis
To: gmx-users at gromacs.org

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  I study on molecular dynamics simulations of organic molecules. I want to learn that Is there an excel-like program that accepts more data set ( for instance output info for 5000 records ) in order to make analysis ? Could you please give me some suggestions about this issue ?

 
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Excel is best at a small number of fixed data sets, or where you have the resources to build some kind of automated import mechanism and the capacity to program custom analysis functions as required. However running some magic macro to import and analyze your data simply doesn't scale to 5000 data sets. Were you to go to all that trouble, you may as well use a tool more suited to the task. Serious numerical work is more often done in R, S, SPSS, Matlab or such, simply because Excel is a generic tool and will not be able to support all specialized needs. Excel's default plot formats are particularly unsuited to scientific needs.

GROMACS provides a large number of command-line tools, which can do most tasks most users want to do. Learning to write simple shell scripts to loop over whatever is creating your 5000 records is a very worthwhile investment for future running and analysis of calculations. gnuplot or xmgrace are desirable plotting tools in this context, though you should check the GROMACS wiki for more suggestions.

Mark

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