Re: namdplot: command not found

From: bo baker (bo.bybaker_at_gmail.com)
Date: Tue Oct 11 2005 - 18:56:10 CDT

Hello:

Thank you very much for your suggestions. Yes, I use Mac OS X. I
downloaded the 'namdplot' script from the NAMD/utilities. And I have
the .log file in the same directory. Then I try to call 'namdplot
TEMP pbr1.log' as the tutorial suggested. But the computer can't
recognize 'namdplot' command. I guess that some commands need to be
added before 'namdplot'. Here is how I did:

[mriv209-01:~/desktop] bo% namdplot
tcsh: namdplot: Command not found.
[mriv209-01:~/desktop] bo% namdplot TEMP pdr1.log
tcsh: namdplot: Command not found.

I don't have experience to wrtie a program in unix. Can anyone suggest
me how to modify the 'namdplot' script , so I can use it for the Mac?
I don't have 'xmgrace' in the computer. I would like to write it into
text file. So I can convert the data with other graph program later.

I have included the 'namdplot' script as an attachment. Your help will
be very appreciated.

Bo

On 10/11/05, Pawel Weronski <pawel_at_cnls.lanl.gov> 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 file.
>
> Pawel
>
>
> 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 and
> >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 found.
> >
> >I am not sure which part I did wrong. How the 'namdplot' woks.
> >
> >Thank you for your help
> >
> >Bo
> >
> >
>
>
>


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