Re: [gmx-users] Analysis of enssemble of MD trajectories
Justin, Francesco, thanks for advises. James 2012/9/21 Justin Lemkul jalem...@vt.edu: On 9/21/12 2:11 AM, James Starlight wrote: Dear collegues Thank for advices. Indeed Gromacs is able to analyse two trajectories with g_rms ( with the flags -f and -f2 ) but as the result I've obtain graph with one rmsd plot so I'm not sure about implementation of that method. So I think that the algorithm proposed by Justin was exactly what I need. But I'm not sure also how I could do such ploating of results of the different g_rms analyses to one common graph ( when I analyse new trajectory and save it by the -o result.xvg if the result.xvg was already exist the old graph is back up to the #result.xvg# etc ). Choose new file names each time. If you have, for instance, result1.xvg, result2.xvg, and result3.xvg, just load them in XmGrace: xmgrace result*.xvg They will all appear in the same plotting area. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Analysis of enssemble of MD trajectories
Dear collegues Thank for advices. Indeed Gromacs is able to analyse two trajectories with g_rms ( with the flags -f and -f2 ) but as the result I've obtain graph with one rmsd plot so I'm not sure about implementation of that method. So I think that the algorithm proposed by Justin was exactly what I need. But I'm not sure also how I could do such ploating of results of the different g_rms analyses to one common graph ( when I analyse new trajectory and save it by the -o result.xvg if the result.xvg was already exist the old graph is back up to the #result.xvg# etc ). James 2012/9/20 lloyd riggs lloyd.ri...@gmx.ch: Dear Dr. I might be wrong, but I think you can use g_rms with two seperate trj files, and it takes the rms from the starting structure of the first one. In which case you would have to decide which is the reference, and then just do it three times. Theres also auxiliarry software which has plugins for this, such as VMD, Pymol, or even O run in some sort of batch. In pymol I know it can be run as a script, but you need all saved pdb files extracted from each trj, so would be a bit large and pain. with the VMD it has plugins for them, but I only played with it once. If you only want to look at beginning and end rms from say the start and end for all traj-using just a couple pdb at either end would be easy in pymol and O. There is also these new tools I found in Bio R (its called Bio3D if you look on the web for the freeware) , which are all scripts that I tried once, which work as well, mostly the take a reference structure and parse the pdbs output from a trj (if you write out each individually) but there values are different but directtly correlatable (ie say 1.6 from the former and something like 80% is cranked out by the later Vs 0.4 and 5% meaning no change) Hope that helps, and if I am wrong about something somone corrects me. Stephan Watkins Original-Nachricht Datum: Thu, 20 Sep 2012 14:06:40 +0400 Von: James Starlight jmsstarli...@gmail.com An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: [gmx-users] Analysis of enssemble of MD trajectories Dear Gromacs Users! I'm working with the enssemble of the MD trajectories calculated for the common protein with the differences in the initial conditions in the case of each trajectory. Now I'd like to perform analysis of that enssemble of data. For example I'de like to obtain RMSD as well as RMSF graphs calculated from all trajectories in one common graph for comparison of the dynamics of the systems. I've used trjcat on my 4 trajectories to obtain one merged trajectory multi.xtc and than tried to calculate RMSD for that multi.xtc but the resulted graph was wrong. trjcat -f md_150ns.xtc md_320ns.xtc sd_125.xtc sd_75ns.xtc -cat -tu ps -o multi.xtc Is there any other way to do such analysis of several trajectories in common graph? James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Analysis of enssemble of MD trajectories
Hi, 2012/9/21 James Starlight jmsstarli...@gmail.com Dear collegues Thank for advices. Indeed Gromacs is able to analyse two trajectories with g_rms ( with the flags -f and -f2 ) but as the result I've obtain graph with one rmsd plot so I'm not sure about implementation of that method. In this case it computes the n1*n2 rmsd matrix! Each frame of the first trajectory is compared with the second trajectory. So I think that the algorithm proposed by Justin was exactly what I need. But I'm not sure also how I could do such ploating of results of the different g_rms analyses to one common graph ( when I analyse new trajectory and save it by the -o result.xvg if the result.xvg was already exist the old graph is back up to the #result.xvg# etc ). James 2012/9/20 lloyd riggs lloyd.ri...@gmx.ch: Dear Dr. I might be wrong, but I think you can use g_rms with two seperate trj files, and it takes the rms from the starting structure of the first one. In which case you would have to decide which is the reference, and then just do it three times. Theres also auxiliarry software which has plugins for this, such as VMD, Pymol, or even O run in some sort of batch. In pymol I know it can be run as a script, but you need all saved pdb files extracted from each trj, so would be a bit large and pain. with the VMD it has plugins for them, but I only played with it once. If you only want to look at beginning and end rms from say the start and end for all traj-using just a couple pdb at either end would be easy in pymol and O. There is also these new tools I found in Bio R (its called Bio3D if you look on the web for the freeware) , which are all scripts that I tried once, which work as well, mostly the take a reference structure and parse the pdbs output from a trj (if you write out each individually) but there values are different but directtly correlatable (ie say 1.6 from the former and something like 80% is cranked out by the later Vs 0.4 and 5% meaning no change) Hope that helps, and if I am wrong about something somone corrects me. Stephan Watkins Original-Nachricht Datum: Thu, 20 Sep 2012 14:06:40 +0400 Von: James Starlight jmsstarli...@gmail.com An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: [gmx-users] Analysis of enssemble of MD trajectories Dear Gromacs Users! I'm working with the enssemble of the MD trajectories calculated for the common protein with the differences in the initial conditions in the case of each trajectory. Now I'd like to perform analysis of that enssemble of data. For example I'de like to obtain RMSD as well as RMSF graphs calculated from all trajectories in one common graph for comparison of the dynamics of the systems. I've used trjcat on my 4 trajectories to obtain one merged trajectory multi.xtc and than tried to calculate RMSD for that multi.xtc but the resulted graph was wrong. trjcat -f md_150ns.xtc md_320ns.xtc sd_125.xtc sd_75ns.xtc -cat -tu ps -o multi.xtc Is there any other way to do such analysis of several trajectories in common graph? James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Analysis of enssemble of MD trajectories
On 9/21/12 2:11 AM, James Starlight wrote: Dear collegues Thank for advices. Indeed Gromacs is able to analyse two trajectories with g_rms ( with the flags -f and -f2 ) but as the result I've obtain graph with one rmsd plot so I'm not sure about implementation of that method. So I think that the algorithm proposed by Justin was exactly what I need. But I'm not sure also how I could do such ploating of results of the different g_rms analyses to one common graph ( when I analyse new trajectory and save it by the -o result.xvg if the result.xvg was already exist the old graph is back up to the #result.xvg# etc ). Choose new file names each time. If you have, for instance, result1.xvg, result2.xvg, and result3.xvg, just load them in XmGrace: xmgrace result*.xvg They will all appear in the same plotting area. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Analysis of enssemble of MD trajectories
Dear Gromacs Users! I'm working with the enssemble of the MD trajectories calculated for the common protein with the differences in the initial conditions in the case of each trajectory. Now I'd like to perform analysis of that enssemble of data. For example I'de like to obtain RMSD as well as RMSF graphs calculated from all trajectories in one common graph for comparison of the dynamics of the systems. I've used trjcat on my 4 trajectories to obtain one merged trajectory multi.xtc and than tried to calculate RMSD for that multi.xtc but the resulted graph was wrong. trjcat -f md_150ns.xtc md_320ns.xtc sd_125.xtc sd_75ns.xtc -cat -tu ps -o multi.xtc Is there any other way to do such analysis of several trajectories in common graph? James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Analysis of enssemble of MD trajectories
On 9/20/12 6:06 AM, James Starlight wrote: Dear Gromacs Users! I'm working with the enssemble of the MD trajectories calculated for the common protein with the differences in the initial conditions in the case of each trajectory. Now I'd like to perform analysis of that enssemble of data. For example I'de like to obtain RMSD as well as RMSF graphs calculated from all trajectories in one common graph for comparison of the dynamics of the systems. I've used trjcat on my 4 trajectories to obtain one merged trajectory multi.xtc and than tried to calculate RMSD for that multi.xtc but the resulted graph was wrong. trjcat -f md_150ns.xtc md_320ns.xtc sd_125.xtc sd_75ns.xtc -cat -tu ps -o multi.xtc Is there any other way to do such analysis of several trajectories in common graph? I think what you want is not concatenation, but rather simultaneous display. Analyze each trajectory separately and simply plot the data in one graph, i.e. 4 different RMSD traces in one panel. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Analysis of enssemble of MD trajectories
Dear Dr. I might be wrong, but I think you can use g_rms with two seperate trj files, and it takes the rms from the starting structure of the first one. In which case you would have to decide which is the reference, and then just do it three times. Theres also auxiliarry software which has plugins for this, such as VMD, Pymol, or even O run in some sort of batch. In pymol I know it can be run as a script, but you need all saved pdb files extracted from each trj, so would be a bit large and pain. with the VMD it has plugins for them, but I only played with it once. If you only want to look at beginning and end rms from say the start and end for all traj-using just a couple pdb at either end would be easy in pymol and O. There is also these new tools I found in Bio R (its called Bio3D if you look on the web for the freeware) , which are all scripts that I tried once, which work as well, mostly the take a reference structure and parse the pdbs output from a trj (if you write out each individually) but there values are different but directtly correlatable (ie say 1.6 from the former and something like 80% is cranked out by the later Vs 0.4 and 5% meaning no change) Hope that helps, and if I am wrong about something somone corrects me. Stephan Watkins Original-Nachricht Datum: Thu, 20 Sep 2012 14:06:40 +0400 Von: James Starlight jmsstarli...@gmail.com An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: [gmx-users] Analysis of enssemble of MD trajectories Dear Gromacs Users! I'm working with the enssemble of the MD trajectories calculated for the common protein with the differences in the initial conditions in the case of each trajectory. Now I'd like to perform analysis of that enssemble of data. For example I'de like to obtain RMSD as well as RMSF graphs calculated from all trajectories in one common graph for comparison of the dynamics of the systems. I've used trjcat on my 4 trajectories to obtain one merged trajectory multi.xtc and than tried to calculate RMSD for that multi.xtc but the resulted graph was wrong. trjcat -f md_150ns.xtc md_320ns.xtc sd_125.xtc sd_75ns.xtc -cat -tu ps -o multi.xtc Is there any other way to do such analysis of several trajectories in common graph? James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
