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 ] >> 457 458 587 >> 457 458 737 >> >> And my hbmap.xpm file indeed contains two entries (following the enumeration >> of x-axis values/times): >> >> "ooooooooooooooo oooooooooooooooooooo oo oooo ooooooooooo >> oooooooooooooooooooooooooooooooooo o oooooooooooooooo ooo >> oooooooooooooooooooooooooooooooooooooo ooooo ooo oooooo o oooooooo ooooo >> oooooo", >> " >> 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 list gmx-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 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing list gmx-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
