Re: 'cutting' colvars.traj file

From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Tue May 03 2011 - 05:55:42 CDT

Thanks a lot Bjoern,

I'll take the script and try immoderately, of course let you know about
results.

Sincerely

Branko

On 5/3/2011 12:45 PM, Bjoern Olausson wrote:
> On Monday 02 May 2011 19:34:26 you wrote:
>> Hi Bjoern,
>>
>> Unfortunately, same problem in Linux, I suppose that "header" line in
>> colvars.traj file could be a problem, so I try to delete this line
>> manually, but file is huge and could not be edited because I have no
>> enough memory in computer (still configuration is OK). Please let me
>> know which version of python you use in order to try to really be able
>> to use script. Out the script problem, I simply try to obtain rgyr (that
>> I use as one of colvars) for my simulations and very obviously that NAMD
>> "write" this data (numerical values of rgyr) in different way comparing
>> to tools that I am able to use for analysis (VMD with script, VegaZZ,
>> PluMed). Because of that I was really satisfied when conclude that 2.8
>> indeed write colvars.traj, you see the rest of story..
>>
>> Kind regards
> Regarding your tries under Windows/Linux:
> No matter what OS you use, start cattraj.py with python and not from within
> the python shell. You approach is completely wrong. The same syntax applies to
> Windows and Linux:
>
> If Python is in the Windows/Linux executable path type:
> python cattraj.py -f 1 -l 500 -s 2 -i test.traj -o test.out
>
> If Python is not in the Windows/Linux executable path, type:
> /your/path/to/python cattraj.py -f 1 -l 500 -s 2 -i test.traj -o test.out
>
>
> The header has nothing to do with my script.
> My script is "stupid", it simply counts lines and ignores commented (#) lines.
> Thats it. You could basically run this script on any file, even on some lyrics
> text, and it would print out something.
>
> Memory shouldn't be a problem with my script, since I read a line and dump it
> to the new file, I don't glob the entire file to memory. This might not be the
> fastest way, but spares memory.
>
> I am using Python 2.6 but it works with 2.7 and 3.1.
> As you can see it works for me with all versions (for python 3 I had to change
> the print syntax slightly, or simply use 2to3 to convert it).
>
> I uploaded a newer version (v1.1) with cleaner indentation (Your error might
> be related) and a default output file value of "cattraj.out.traj" so the "-o"
> option is no longer mandatory.
> http://olausson.de/downloads/view.download/6/13
>
> Please keep in mind that Linux uses UNIX-Style line-breaks, just in case you
> want to edit the file under Windows.
>
>
> ~~~~~Python 2.6.6~~~~~
> #python2.6 cattraj.py -f 1 -l 500 -s 2 -i test.traj -o test.out
>
> Reading colvars.traj
> Frames - r: 500
> Frames - w: 250
>
> -----------------------------------
> -----------------------------------
> Overall frames - r: 500
> Overall frames - w: 250
>
>
> ~~~~~Python 2.7.1~~~~~
> #python2.7 cattraj.py -f 1 -l 500 -s 2 -i test.traj -o test.out
>
> Reading test.traj
> Frames - r: 500
> Frames - w: 250
>
> -----------------------------------
> -----------------------------------
> Overall frames - r: 500
> Overall frames - w: 250
>
>
> ~~~~~Python 3.1.3~~~~~
> python3.1 cattraj3.py -f 1 -l 500 -s 2 -i test.traj -o test.out
>
> Reading test.traj
> Frames - r: 500
> Frames - w: 250
>
> -----------------------------------
> -----------------------------------
> Overall frames - r: 500
> Overall frames - w: 250
>
>
>
> Cheers,
> Bjoern
>

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