CCL: help needed
- From: Serena Povia <sp422:hermes.cam.ac.uk>
- Subject: CCL: help needed
- Date: Mon, 1 May 2006 14:06:10 +0100 (BST)
Sent to CCL by: Serena Povia [sp422(_)hermes.cam.ac.uk]
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
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.
On Mon, 1 May 2006, Richard L. Wood rwoodphd:msn.com wrote:
Sent to CCL by: "Richard L. Wood" [rwoodphd##msn.com]
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!