From owner-chemistry@ccl.net Tue May 2 12:06:01 2006 From: "Peter Pinski peter.pinski-forum,,web.de" To: CCL Subject: CCL: help needed Message-Id: <-31655-060502105557-14814-s3MeTf3BJvDvEX8NgB5rVw,,server.ccl.net> X-Original-From: Peter Pinski Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15 Date: Tue, 02 May 2006 16:55:57 +0200 MIME-Version: 1.0 Sent to CCL by: Peter Pinski [peter.pinski-forum . web.de] Hi, a bourne shell, perl, python etc. run on windows easily using cygwin. (www.cygwin.com) Peter Marcin Krol mykrol_._cyf-kr.edu.pl schrieb: > Sent to CCL by: Marcin Krol [mykrol^cyf-kr.edu.pl] > Hi Richard, > If you have access to a linux/unix machine try typing this command on the > command prompt: > > grep "ENERGY:" namd_heat.out | awk '{print $12}' | sort -n -k1 | tail -1 > this should give you the lowest value > > grep "ENERGY:" namd_heat.out | awk '{print $12}' | sort -n -k1 | head -1 > this gives you highest value > > change namd_heat.out to the name of your file. I analyzed an output file >> from NAMD 2.5 for Linux-i686-TCP, but I hope that your namd produces an > identical file. Namd Total Energy is in column 12, if you want to analyze > different quantity (eg. temperature) change $12 to something else. > > If you don't have access to a linux machine try a script like this in > python (I don't know how to install python on windows): > > import string > > out_file = open("namd_heat.out",'r') > data = out_file.readlines() > out_file.close() > > energy = [] > for line in data: > try: > if line.split()[0] == "ENERGY:": > energy.append(eval(line.split()[11])) > except: > pass > > energy.sort() > print("the lowest energy value is %f\nthe highest energy value is %f\n" > %(energy[0], energy[-1])) > > Hope this helps > Marcin > > > > On Mon, 1 May 2006, RICHARD JILL WOOD rwoodphd++msn.com wrote: > >> 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/> > > >