From owner-chemistry@ccl.net Mon May  1 11:01:01 2006
From: "donna : dbkonline.com" <owner-chemistry-,-server.ccl.net>
To: CCL
Subject: CCL: help needed
Message-Id: <-31640-060501093103-10873-43/87Ytm/1lB86ESgOEupQ-,-server.ccl.net>
X-Original-From: donna~!~dbkonline.com
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Date: Mon, 01 May 2006 07:53:38 -0500
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Sent to CCL by: donna[]dbkonline.com
Quoting "Richard L. Wood rwoodphd:msn.com" <owner-chemistry()ccl.net>:


What about a perl script or something ?

When we did MD simulations of huge trajectories that's what we did... you can
either do it on the fly - if you just want to get the lowest ... or create a
database a sort it.

Donna

DBK Development, LLC



> Sent to CCL by: "Richard L. Wood" [rwoodphd##msn.com]
> Hi all,
>
> This question isn't a direct computational chemistry question, but an 
> indirect one.  So please bear with me.
>
> I'm trying to analyze the output of a 1 nanosecond MD calculation 
> that I ran using the program NAMD.  Since it's a text file, I could 
> use MS Excel to open it and sort the energies from lowest to highest 
> value, which is what I would like to do.  However, MS Excel has a 
> limit of about 65000 lines of text (or rows) that a file can contain. 
>  Mine has 2000000 lines of text, so that my file is too big.  My 
> workaround is to open the file in MS Word, and cut it into pieces 
> that can be opened in MS Excel.  Then I can find the minimum energy 
> fro each piece, save that value, and then when done, find the overall 
> minimum.  Once I've done this, I can find the corresponding frame 
> number in the file that contained it, go to the trajectory and save 
> those coordinates.
>
> However, as you can imagine, this isn't a very efficient process.  My 
> simulation takes about 2 and half hours or so to run, while this 
> analysis takes about two hours to do.  I can therefore do about one 
> of these in a day, as I have another non-computational "job" that I 
> am doing.  At some point, I will be running some smalled 
> calculations, which will take much less than two hours to run, and so 
> the analysis will take longer than the simulation!
>
> My question is this:  does anyone know of a spreadsheat program where 
> I can a) import a text file of more than 65000 rows easily, b) can 
> sort a given column of that file, and c) works under Windows and is 
> free?  I've tried Quattro Pro, and all the file comes out in a single 
> row!
>
> TIA,
> Richard>
>
>
>