PyMDLog is a Python-powered tool for analyzing log files generated by molecular dynamics (MD) simulation packages.

I use MD packages, such as Amber and NAMD, in my research work. Each of them generates log files (mdout in Amber's terminology) while computing. Properties of the simulation system are recorded in the files. There are existing scripts for parsing them, like process_mdout.perl for Amber and namdplot for NAMD. However, I'm not satisfied with them. So I wrote this tool and made it publicly available. I found it useful and hope it is also helpful to you.

• Python 2.7, 3.2-3.4

• matplotlib (optional, for plotting)

Once you have satisfied the requirements, you can extract the downloaded source file to a scratch directory. From the directory where setup.py is, run this command from the command prompt:

$ python setup.py install

Make sure PYTHONHOME/Scripts is in the PATH environment variable. Then run this command:

$ pymdlog

You will see a GUI which is fairly self-explanatory:

Or if you want to use the command-line mode, do things like this:

$ pymdlog -i 1.out 2.out -t amber -x TIME -y Etot "1-4 NB" -o result.dat

$ pymdlog -i 1.log 2.log -t namd -x TS -y BOND ANGLE -f result.png

For more information about the arguments, run

$ pymdlog -h

If you haven't installed matplotlib or don't like the generated figure, you can use the output file with your favorite plotting software:

• Simple for Gnuplot, xmgrace, R (read.table with header=FALSE), Origin

• CSV for Excel

The above-mentioned have been tested, however, other programs should be compatible too.

If you have any questions about using this program or find a bug, please feel free to contact me via email: teffliu@hotmail.com