From: Pawel Weronski (pawel_at_cnls.lanl.gov)
Date: Wed Oct 12 2005 - 08:57:32 CDT
Hi Bo,
I don't know how it should work on Mac. Do you need to give a path
before the file name, like on Unix? I mean, maybe you need to use the
command "./namdplot TEMP pdr1.log"?
Pawel
bo baker wrote:
>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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