From: Robert Brunner (rbrunner_at_uiuc.edu)
Date: Tue Oct 11 2005 - 10:32:00 CDT
Actually, the tutorials are designed to run on the Mac, using a
number of Unix utilities. The scripts they use work on both OS X and
Linux, for the most part.
The namdplot script is available at
However, it uses the Grace plotting program (xmgrace) which you may
need to install on your Mac. The DarwinPorts system somewhat
simplifies installation of programs like xmgrace.
Note that to install Grace, you may also need X11, from your Mac OS X
installation CD, and the X11 SDK, from the Apple XCode disk. XCode
comes with OS X, and is also available for download from the Apple
On Oct 11, 2005, at 8:22 AM, Pawel Weronski wrote:
> Hi Bo,
> It seems to me that you work in Mac, don't you? As far as I know
> the scripts work in Linux/Unix only (there are system specific
> commands inside). Just try to write a simple program in any
> language to extract all lines starting with "TEMP:" from your data
> bo baker wrote:
>> Hello, NAMD:
>> I would like to analysis the result from a NAMD MD run. According to
>> the NAMD tutorial, 'namdpot' is the command to extract TEMP, TOTAL
>> PRESS information from the .log file. Here is how I did:
>> bo% cd /Applications/NAMD_2.6b1_MacOSX-PPC
>> bo% namdplot TEMP pbr1.log
>> tcsh: namdplot: Command not found.
>> bo% /Applications/NAMD_2.6b1_MacOSX-PPC/namdplot TEMP pbr1.log
>> tcsh: /Applications/NAMD_2.6b1_MacOSX-PPC/namdplot: Command not
>> I am not sure which part I did wrong. How the 'namdplot' woks.
>> Thank you for your help
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