problems with namdplot fixed by using new plotting program

From: Cheri M Turman (
Date: Tue Apr 27 2004 - 16:34:42 CDT

Just wanted to let everyone know that I was never able to get namdplot
or Gadi's programs to work on my computer. Therefore, Eric Williams
from our lab wrote a program called NAMD log parser to help me overcome
this problem. He wrote it in java which should be more cross-platform
compatible, but will be a little slower. Please feel free to use this
if you have the same problems I did. You can get the program from

Make sure you at least have java 1.4. (We had tested this with sun
java 1.4.2 so at minimum you should need java 1.4) There are still
some bugs in what you can see on the plot within this program but at
least it can help to easily export the data in spreadsheet format to
your favorite graphing program. Also, there is no print function in
the program yet. Therefore, the graphing part is just for
visualization at the moment. Eric is working on that. I hope this can
be of help to anyone else struggling with this!


   Cheri M. Turman
   Graduate Student
   University of Texas-Houston Medical School
    6431 Fannin
    Houston, TX 77030 USA

    Ph.: 713-500-6126
    Fax: 713-500-0652

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