[gmx-users] question about g_rmsdist II
Sorry, since I hadn't any answer to my question yet, I'm resending it to give it visibility! Thanks, Fabrizio --- Messaggio inoltrato --- Da: Fabrizio Mancinelli [EMAIL PROTECTED] A: gmx-users@gromacs.org Oggetto: question about g_rmsdist Data: Mon, 14 May 2007 18:52:54 +0200 Dear all, I would like to have some elucidation about g_rmsdist output. Optionally, it outputs three matrices with the options -rms, -mean and - scl. Questions are: 1) Exploring .xpm files, I see there is a letter code which converts color exa-codes to letters to values. The resolution is tunable with option -nlevels, but the range is delimited by the highest calculated value. Is there a way to assign a fixed range (in order, e.g., to compare different trajectories of the same protein)? 2) -rms output, I guess, is the deviation from average distance, over time, for each atom couple. I see my matrix is full of 0's. I expected 0's on the principal diagonal (distance of an atom from itself is obviously always zero), but others? It should mean atoms' distances RMSD are 0, that is they do not deviate... but they don't look that fixed at all from the trajectory! This is even more surprisingly in the -mean output, which should contain, I guess, atom distances averaged over time. In that case there are lots of 0's too. Maybe my I guess are wrong... 3) What is, actually, -scl output? Thanks in advance to anybody who will answer. Fabrizio ___ 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] question about g_rmsdist II
Fabrizio Mancinelli wrote: Sorry, since I hadn't any answer to my question yet, I'm resending it to give it visibility! If you don't get any luck, remember that the source code is available for a reason :-) --- Messaggio inoltrato --- Da: Fabrizio Mancinelli [EMAIL PROTECTED] A: gmx-users@gromacs.org Oggetto: question about g_rmsdist Data: Mon, 14 May 2007 18:52:54 +0200 Dear all, I would like to have some elucidation about g_rmsdist output. Optionally, it outputs three matrices with the options -rms, -mean and - scl. Questions are: 1) Exploring .xpm files, I see there is a letter code which converts color exa-codes to letters to values. The resolution is tunable with option -nlevels, but the range is delimited by the highest calculated value. Is there a way to assign a fixed range (in order, e.g., to compare different trajectories of the same protein)? There was discussion on the list of implementing a way to write a binary or ascii matrix. This would make it easy to do the kind of comparison I think you want to do. Check the archives for the resolution, but if there was one suitable for your needs, you'd need to use the CVS version of this utility. 2) -rms output, I guess, is the deviation from average distance, over time, for each atom couple. I see my matrix is full of 0's. I expected 0's on the principal diagonal (distance of an atom from itself is obviously always zero), but others? It should mean atoms' distances RMSD are 0, that is they do not deviate... but they don't look that fixed at all from the trajectory! This is even more surprisingly in the -mean output, which should contain, I guess, atom distances averaged over time. In that case there are lots of 0's too. Maybe my I guess are wrong... You've certainly got the wrong handle on -mean. Check the man page. 3) What is, actually, -scl output? Don't know. Mark ___ 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] question about g_rmsdist II
17 maj 2007 kl. 15.49 skrev Mark Abraham: Fabrizio Mancinelli wrote: Sorry, since I hadn't any answer to my question yet, I'm resending it to give it visibility! If you don't get any luck, remember that the source code is available for a reason :-) --- Messaggio inoltrato --- Da: Fabrizio Mancinelli [EMAIL PROTECTED] A: gmx-users@gromacs.org Oggetto: question about g_rmsdist Data: Mon, 14 May 2007 18:52:54 +0200 Dear all, I would like to have some elucidation about g_rmsdist output. Optionally, it outputs three matrices with the options -rms, -mean and - scl. Questions are: 1) Exploring .xpm files, I see there is a letter code which converts color exa-codes to letters to values. The resolution is tunable with option -nlevels, but the range is delimited by the highest calculated value. Is there a way to assign a fixed range (in order, e.g., to compare different trajectories of the same protein)? There was discussion on the list of implementing a way to write a binary or ascii matrix. This would make it easy to do the kind of comparison I think you want to do. Check the archives for the resolution, but if there was one suitable for your needs, you'd need to use the CVS version of this utility. 2) -rms output, I guess, is the deviation from average distance, over time, for each atom couple. I see my matrix is full of 0's. I expected 0's on the principal diagonal (distance of an atom from itself is obviously always zero), but others? It should mean atoms' distances RMSD are 0, that is they do not deviate... but they don't look that fixed at all from the trajectory! This is even more surprisingly in the -mean output, which should contain, I guess, atom distances averaged over time. In that case there are lots of 0's too. Maybe my I guess are wrong... You've certainly got the wrong handle on -mean. Check the man page. 3) What is, actually, -scl output? I don't use g_rmsdist much, but the -h option tells me that g_rmsdist can also produce matrices of the rms distances, rms distances scaled with the mean distance and the mean distances and matrices with NMR averaged distances (1/r^3 and 1/r^6 averaging)., which is a good clue. /Erik Don't know. Mark ___ 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 ___ Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys ___ 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
