From: "Serena Povia sp422]|[hermes.cam.ac.uk"
<owner-chemistry~~ccl.net>
Reply-To: "CCL Subscribers" <chemistry~~ccl.net>
To: "Wood, Richard L. " <rwoodphd~~msn.com>
Subject: CCL: help needed
Date: Mon, 1 May 2006 09:11:09 -0400
Sent to CCL by: Serena Povia [sp422(_)hermes.cam.ac.uk]
Dear Rich,
I'm sorry to tell you that your problem could be *easily* solved in
unix, writing a bash/perl script to grep the energy line you're
interested in some way, and sort them, and go back to pick up the
energies. It's really a matter of 50 lines of code at
most and once it's done everything will be authomatic for the following
calculations.
if you run your calculations on a unix machine you could even run the
analysis script on it an then get your nice data back in windows. I'm
learning bash myself and I'll be happy to help.
best, serena
On Mon, 1 May 2006, Richard L. Wood rwoodphd:msn.com wrote:
> 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>