Re: [gmx-users] Ordering of hydrogen bonds in -hbn and -hbm output in g_hbond
I think the confusion arises form 15 aug 2012 kl. 22.53 skrev Justin Lemkul: On 8/15/12 4:49 PM, Andrew DeYoung wrote: Hi, I am a novice user of g_hbond (actually, I am using double precision -- g_hbond_d -- but I think all of the parameters should be the same). I would like to use the output of the -hbn switch (which generates hbond.ndx) in tandem with the -hbm switch (which generates an existence matrix hbmap.xpm) to determine, using my own script, which hydrogen bonds exist at each timestep in my trajectory. My question is, how does the order of entries in the [ hbonds ] section in hbond.ndx relate to the order of entries in hbmap.xpm? I am running Gromacs 4.5.5. The man page for g_hbond_d clearly states: -hbm: existence matrix for all hydrogen bonds over all frames... . Ordering is identical to that in -hbn index file. However, I did a test of a system with two hydrogen bonds (which exist at different times), and it seems (although I am not at all certain) that the opposite is actually true. My hbond.ndx file contains the following section at the end of the file: [ hbonds ] 457458587 457458737 And my hbmap.xpm file indeed contains two entries (following the enumeration of x-axis values/times): ooo oo ooo oo o ooo oo o ooo oo o o oo, o o which tells me that one of the hydrogen bonds exists for a very large fraction of the trajectory, whereas the other exists for only two timesteps during the trajectory. I visualized the system in VMD. I clearly see that the hydrogen bond 457 458 737 (i.e., the _first_ entry in the [ hbonds ] section of the index file) is the one that exists for the vast majority of the trajectory. Conversely, the hydrogen bond 457 458 587 is clearly the one that exists for only two timesteps in the trajectory. Based on this, it seems that the top-to-bottom order of hbmap.xpm is actually _opposite_ that of the [ hbonds ] section in hbond.ndx. Has anyone else tested this? If so, what conclusion did you reach about the ordering in the -hbn and -hbm output files. Or do you see a mistake in my reasoning above? One assumption I have made in my above reasoning is that o means the hydrogen bond exists, whereas means the hydrogen bond does NOT exist. I am not 100% sure that this is correct, but plotting the matrix as an EPS file using xpm2ps seems to say that I am correct. Your interpretation of the contents is correct. The first entry in hbonds.ndx is also the first entry in the .xpm file, which is the last line (index zero, hence the first entry). I have a script that calculates hydrogen bond existence time (plot_hbmapl.pl) from these two files if you want to confirm your outcome. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html -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 * Only plain text messages are allowed! * 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Ordering of hydrogen bonds in -hbn and -hbm output in g_hbond
Hi, I think the confusion arises from how the xpm data is displayed. If you have the hb-index on the y-axis in a plot with the positive y-direction pointing upwards (as in most plots), then the first line in the xpm file is actually displayed at the bottom. For matrices, however, the indexing starts from the top, not the bottom. Perhaps we should aim at making this more clear in the program output. It's confusing and a reoccurring topic on the user list. Erik 15 aug 2012 kl. 22.53 skrev Justin Lemkul: On 8/15/12 4:49 PM, Andrew DeYoung wrote: Hi, I am a novice user of g_hbond (actually, I am using double precision -- g_hbond_d -- but I think all of the parameters should be the same). I would like to use the output of the -hbn switch (which generates hbond.ndx) in tandem with the -hbm switch (which generates an existence matrix hbmap.xpm) to determine, using my own script, which hydrogen bonds exist at each timestep in my trajectory. My question is, how does the order of entries in the [ hbonds ] section in hbond.ndx relate to the order of entries in hbmap.xpm? I am running Gromacs 4.5.5. The man page for g_hbond_d clearly states: -hbm: existence matrix for all hydrogen bonds over all frames... . Ordering is identical to that in -hbn index file. However, I did a test of a system with two hydrogen bonds (which exist at different times), and it seems (although I am not at all certain) that the opposite is actually true. My hbond.ndx file contains the following section at the end of the file: [ hbonds ] 457458587 457458737 And my hbmap.xpm file indeed contains two entries (following the enumeration of x-axis values/times): ooo oo ooo oo o ooo oo o ooo oo o o oo, o o which tells me that one of the hydrogen bonds exists for a very large fraction of the trajectory, whereas the other exists for only two timesteps during the trajectory. I visualized the system in VMD. I clearly see that the hydrogen bond 457 458 737 (i.e., the _first_ entry in the [ hbonds ] section of the index file) is the one that exists for the vast majority of the trajectory. Conversely, the hydrogen bond 457 458 587 is clearly the one that exists for only two timesteps in the trajectory. Based on this, it seems that the top-to-bottom order of hbmap.xpm is actually _opposite_ that of the [ hbonds ] section in hbond.ndx. Has anyone else tested this? If so, what conclusion did you reach about the ordering in the -hbn and -hbm output files. Or do you see a mistake in my reasoning above? One assumption I have made in my above reasoning is that o means the hydrogen bond exists, whereas means the hydrogen bond does NOT exist. I am not 100% sure that this is correct, but plotting the matrix as an EPS file using xpm2ps seems to say that I am correct. Your interpretation of the contents is correct. The first entry in hbonds.ndx is also the first entry in the .xpm file, which is the last line (index zero, hence the first entry). I have a script that calculates hydrogen bond existence time (plot_hbmapl.pl) from these two files if you want to confirm your outcome. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html -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 * Only plain text messages are allowed! * 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Ordering of hydrogen bonds in -hbn and -hbm output in g_hbond
Hi, I am a novice user of g_hbond (actually, I am using double precision -- g_hbond_d -- but I think all of the parameters should be the same). I would like to use the output of the -hbn switch (which generates hbond.ndx) in tandem with the -hbm switch (which generates an existence matrix hbmap.xpm) to determine, using my own script, which hydrogen bonds exist at each timestep in my trajectory. My question is, how does the order of entries in the [ hbonds ] section in hbond.ndx relate to the order of entries in hbmap.xpm? I am running Gromacs 4.5.5. The man page for g_hbond_d clearly states: -hbm: existence matrix for all hydrogen bonds over all frames... . Ordering is identical to that in -hbn index file. However, I did a test of a system with two hydrogen bonds (which exist at different times), and it seems (although I am not at all certain) that the opposite is actually true. My hbond.ndx file contains the following section at the end of the file: [ hbonds ] 457458587 457458737 And my hbmap.xpm file indeed contains two entries (following the enumeration of x-axis values/times): ooo oo ooo oo o ooo oo o ooo oo o o oo, o o which tells me that one of the hydrogen bonds exists for a very large fraction of the trajectory, whereas the other exists for only two timesteps during the trajectory. I visualized the system in VMD. I clearly see that the hydrogen bond 457 458 737 (i.e., the _first_ entry in the [ hbonds ] section of the index file) is the one that exists for the vast majority of the trajectory. Conversely, the hydrogen bond 457 458 587 is clearly the one that exists for only two timesteps in the trajectory. Based on this, it seems that the top-to-bottom order of hbmap.xpm is actually _opposite_ that of the [ hbonds ] section in hbond.ndx. Has anyone else tested this? If so, what conclusion did you reach about the ordering in the -hbn and -hbm output files. Or do you see a mistake in my reasoning above? One assumption I have made in my above reasoning is that o means the hydrogen bond exists, whereas means the hydrogen bond does NOT exist. I am not 100% sure that this is correct, but plotting the matrix as an EPS file using xpm2ps seems to say that I am correct. Thanks so much for your time. Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Ordering of hydrogen bonds in -hbn and -hbm output in g_hbond
On 8/15/12 4:49 PM, Andrew DeYoung wrote: Hi, I am a novice user of g_hbond (actually, I am using double precision -- g_hbond_d -- but I think all of the parameters should be the same). I would like to use the output of the -hbn switch (which generates hbond.ndx) in tandem with the -hbm switch (which generates an existence matrix hbmap.xpm) to determine, using my own script, which hydrogen bonds exist at each timestep in my trajectory. My question is, how does the order of entries in the [ hbonds ] section in hbond.ndx relate to the order of entries in hbmap.xpm? I am running Gromacs 4.5.5. The man page for g_hbond_d clearly states: -hbm: existence matrix for all hydrogen bonds over all frames... . Ordering is identical to that in -hbn index file. However, I did a test of a system with two hydrogen bonds (which exist at different times), and it seems (although I am not at all certain) that the opposite is actually true. My hbond.ndx file contains the following section at the end of the file: [ hbonds ] 457458587 457458737 And my hbmap.xpm file indeed contains two entries (following the enumeration of x-axis values/times): ooo oo ooo oo o ooo oo o ooo oo o o oo, o o which tells me that one of the hydrogen bonds exists for a very large fraction of the trajectory, whereas the other exists for only two timesteps during the trajectory. I visualized the system in VMD. I clearly see that the hydrogen bond 457 458 737 (i.e., the _first_ entry in the [ hbonds ] section of the index file) is the one that exists for the vast majority of the trajectory. Conversely, the hydrogen bond 457 458 587 is clearly the one that exists for only two timesteps in the trajectory. Based on this, it seems that the top-to-bottom order of hbmap.xpm is actually _opposite_ that of the [ hbonds ] section in hbond.ndx. Has anyone else tested this? If so, what conclusion did you reach about the ordering in the -hbn and -hbm output files. Or do you see a mistake in my reasoning above? One assumption I have made in my above reasoning is that o means the hydrogen bond exists, whereas means the hydrogen bond does NOT exist. I am not 100% sure that this is correct, but plotting the matrix as an EPS file using xpm2ps seems to say that I am correct. Your interpretation of the contents is correct. The first entry in hbonds.ndx is also the first entry in the .xpm file, which is the last line (index zero, hence the first entry). I have a script that calculates hydrogen bond existence time (plot_hbmapl.pl) from these two files if you want to confirm your outcome. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html -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 * Only plain text messages are allowed! * 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
