From owner-chemistry@ccl.net Mon May 1 20:35:01 2006 From: "RICHARD JILL WOOD rwoodphd++msn.com" To: CCL Subject: CCL: help needed Message-Id: <-31647-060501103227-31021-1dQNvUFPoxi2TC/DAAuBqg*server.ccl.net> X-Original-From: "RICHARD JILL WOOD" Content-Type: text/plain; format=flowed Date: Mon, 01 May 2006 13:45:09 +0000 Mime-Version: 1.0 Sent to CCL by: "RICHARD JILL WOOD" [rwoodphd+*+msn.com] Hi Serena: Not to sound lazy, but the problem is that I just don't have the "spare time" to write code, in unix, or any other language. I work five days a week at a low paying non-computational chemistry job, and I have two days off to work on this project (which I'm not getting compensated for, obviously) a week, and I'd like to be spending my free time working on the project, as opposed to writing code for it. I'm hoping to get this data, package it together with some other calculations that I did when I was a professional computational chemist, and publish it. Obviously, I'm also looking for another computational chemist position. So, I'd appreciate any help you can offer. Richard >From: "Serena Povia sp422]|[hermes.cam.ac.uk" >Reply-To: "CCL Subscribers" >To: "Wood, Richard L. " >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> > > _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today - it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/