[gmx-users] Ordering of hydrogen bonds in -hbn and -hbm output in g_hbond

[Erik Marklund]

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 ]
>>     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
> 
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-----------------------------------------------
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
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html