Re: [gmx-users] Analyzing a trajectory split over multiple files
Just as a note most analysis tools have a -noxvgr option to output the results without any of the formatting information for grace. Also I still think the easiest way to solve your problem is to just initially use trjcat to concatenate your trajectory, then run the analysis on this. Tom --On Friday, November 28, 2008 05:06:31 +0530 Suman Chakrabarty [EMAIL PROTECTED] wrote: On Fri, Nov 28, 2008 at 4:24 AM, Nicolas [EMAIL PROTECTED] wrote: Suman Chakrabarty a écrit : It would have been much easier if there was some way to concatenate the multiple .xvg files easily. Also, the analysis programs should be able to export the output data in raw 2 (or more) column format without all the formatting statements as an option. Actually, there is: grep -v ^# *.xvg concatenate.xvg The -v ^# will skip all the comment lines of your xvg files. Of course, this assumes that your xvg files are correctly named, i.e. file01.xvg, file02.xvg, etc. With a short shell script, you can easily re-add the comments at the beginning of your concatenate file, renumber the frames correctly, etc. It is more convenient to write a Python or a Perl script to do this kind of stuff, though. Nicolas Thank you very much! I always knew there must be something smart to be done. I should now delve into the nitty-gritty of scripting. grep seems to be a particularly useful tool! :) Regards, Suman. -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Analyzing a trajectory split over multiple files
On Wed, Nov 26, 2008 at 2:19 PM, Omer Markovitch [EMAIL PROTECTED] wrote: On Tue, Nov 25, 2008 at 01:47, Suman Chakrabarty [EMAIL PROTECTED] wrote: Dear all, I have a very long trajectory split over a large number of files. What would be the most efficient way to use the analysis programs over them? Do they support multiple input for trajectory? Or I need to combine all files into a single one anyway? You should analyze each individual part on its own, and output the raw data of the result, then average the parts together. For example - say you are interested in coordination number of molecule X: For each part, output both the total number of X's found, plus the total number of X neighbors found. The coordination number is then the sum of neig. divided by the sum of X's, from ALL parts. It might be an issue if each part has different time length, then averaging the coordination number of each part might give more statistical weigh to short parts then they should have. In other words, you should first collect the data of each part together, and only then avg.. --Omer. Thanks for your response Omer. But I am currently more interested in observing the time evolution of certain properties, e.g. radius of gyration etc. and their histogram over the full trajectory. So I must combine either trajectory files or the output analysis data. It would have been much easier if there was some way to concatenate the multiple .xvg files easily. Also, the analysis programs should be able to export the output data in raw 2 (or more) column format without all the formatting statements as an option. Regards, Suman. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Analyzing a trajectory split over multiple files
Suman Chakrabarty a écrit : On Wed, Nov 26, 2008 at 2:19 PM, Omer Markovitch [EMAIL PROTECTED] wrote: On Tue, Nov 25, 2008 at 01:47, Suman Chakrabarty [EMAIL PROTECTED] wrote: Dear all, I have a very long trajectory split over a large number of files. What would be the most efficient way to use the analysis programs over them? Do they support multiple input for trajectory? Or I need to combine all files into a single one anyway? You should analyze each individual part on its own, and output the raw data of the result, then average the parts together. For example - say you are interested in coordination number of molecule X: For each part, output both the total number of X's found, plus the total number of X neighbors found. The coordination number is then the sum of neig. divided by the sum of X's, from ALL parts. It might be an issue if each part has different time length, then averaging the coordination number of each part might give more statistical weigh to short parts then they should have. In other words, you should first collect the data of each part together, and only then avg.. --Omer. Thanks for your response Omer. But I am currently more interested in observing the time evolution of certain properties, e.g. radius of gyration etc. and their histogram over the full trajectory. So I must combine either trajectory files or the output analysis data. It would have been much easier if there was some way to concatenate the multiple .xvg files easily. Also, the analysis programs should be able to export the output data in raw 2 (or more) column format without all the formatting statements as an option. Actually, there is: grep -v ^# *.xvg concatenate.xvg The -v ^# will skip all the comment lines of your xvg files. Of course, this assumes that your xvg files are correctly named, i.e. file01.xvg, file02.xvg, etc. With a short shell script, you can easily re-add the comments at the beginning of your concatenate file, renumber the frames correctly, etc. It is more convenient to write a Python or a Perl script to do this kind of stuff, though. Nicolas Regards, Suman. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php begin:vcard fn:Nicolas Sapay n:Sapay;Nicolas org:University of Calgary;Biological department adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada email;internet:[EMAIL PROTECTED] title:Post-doctoral fellow tel;work:403-220-6869 x-mozilla-html:TRUE url:http://moose.bio.ucalgary.ca/ version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Analyzing a trajectory split over multiple files
On Fri, Nov 28, 2008 at 4:24 AM, Nicolas [EMAIL PROTECTED] wrote: Suman Chakrabarty a écrit : It would have been much easier if there was some way to concatenate the multiple .xvg files easily. Also, the analysis programs should be able to export the output data in raw 2 (or more) column format without all the formatting statements as an option. Actually, there is: grep -v ^# *.xvg concatenate.xvg The -v ^# will skip all the comment lines of your xvg files. Of course, this assumes that your xvg files are correctly named, i.e. file01.xvg, file02.xvg, etc. With a short shell script, you can easily re-add the comments at the beginning of your concatenate file, renumber the frames correctly, etc. It is more convenient to write a Python or a Perl script to do this kind of stuff, though. Nicolas Thank you very much! I always knew there must be something smart to be done. I should now delve into the nitty-gritty of scripting. grep seems to be a particularly useful tool! :) Regards, Suman. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Analyzing a trajectory split over multiple files
On Tue, Nov 25, 2008 at 01:47, Suman Chakrabarty [EMAIL PROTECTED]wrote: Dear all, I have a very long trajectory split over a large number of files. What would be the most efficient way to use the analysis programs over them? Do they support multiple input for trajectory? Or I need to combine all files into a single one anyway? You should analyze each individual part on its own, and output the raw data of the result, then average the parts together. For example - say you are interested in coordination number of molecule X: For each part, output both the total number of X's found, plus the total number of X neighbors found. The coordination number is then the sum of neig. divided by the sum of X's, from ALL parts. It might be an issue if each part has different time length, then averaging the coordination number of each part might give more statistical weigh to short parts then they should have. In other words, you should first collect the data of each part together, and only then avg.. --Omer. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Analyzing a trajectory split over multiple files
Dear all, I have a very long trajectory split over a large number of files. What would be the most efficient way to use the analysis programs over them? Do they support multiple input for trajectory? Or I need to combine all files into a single one anyway? Please help. Regards, Suman. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Analyzing a trajectory split over multiple files
Suman Chakrabarty a écrit : Dear all, I have a very long trajectory split over a large number of files. What would be the most efficient way to use the analysis programs over them? Do they support multiple input for trajectory? No most of the time, but you can easily analyze each part of your trajectory by embedding the Gromacs command line in a while loop. In Bash, it gives something like: npart=xxx i=0 while [ $i -le $npart ]; do g_xxx ... g_xxx.out i=$[i+1] done Or I need to combine all files into a single one anyway? I guess it depends on the time scale of the phenomenon you want to observe and on how often you have sample your coordinates/velocity/energy during the computation. For a short time scale phenomenon, like bond stretching, you can split your trajectory into pieces of, let say, 5 ns and consider each piece as independent. For a long time scale phenomenon, you will have to split your trajecory in bigger pieces or even merge all the parts. Please help. Regards, Suman. begin:vcard fn:Nicolas Sapay n:Sapay;Nicolas org:University of Calgary;Biological department adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada email;internet:[EMAIL PROTECTED] title:Post-doctoral fellow tel;work:403-220-6869 x-mozilla-html:TRUE url:http://moose.bio.ucalgary.ca/ version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Analyzing a trajectory split over multiple files
Suman Chakrabarty wrote: Dear all, I have a very long trajectory split over a large number of files. What would be the most efficient way to use the analysis programs over them? Do they support multiple input for trajectory? Or I need to combine all files into a single one anyway? Use trjcat to make one trajectory. I believe multiple file I/O is a goal for the future, but I don't believe it is accomplished yet. -Justin Please help. Regards, Suman. -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
