[gmx-users] hbond

Gregory Poon gpoon at gsu.edu
Thu Dec 1 16:58:53 CET 2016

On 12/1/2016 7:45 AM, Justin Lemkul wrote:
> On 12/1/16 7:24 AM, Gregory Man Kai Poon wrote:
>> Hi all:
>> I am trying to use hbond in Gromacs 5.1.4 to analyze water-mediated 
>> hydrogen
>> bonding between two objects simulated in water.  The GROMACS manual 
>> discusses
>> this in a Figure (9.8) - "water insertion". There is nothing in the 
>> online
>> documentation as to how this should be done except a single mention 
>> with the
>> -hbm option, which I tried.  It generated .xpm files such as the one
>> attached.  They open, as far as I can tell, a very vertically 
>> compressed plot
>> which I can make nothing out of.  Attempts to convert them to eps using
>> xpm2eps output similar results.
> You can use an .m2p file to adjust the sizes of the x- and y-axes to 
> make it legible.  The real value is in the data within, though.  You 
> have to map the actual participating groups (the output of of -hbn) 
> with the individual time series in the .xpm from -hbm.
>> So my questions are two-fold: 1) What is happening with the .xpm 
>> files?  2)
>> Am I using the correct hbond option to enumerate water-mediated hydrogen
>> bonds?
> To actually analyze water-mediated H-bonds requires additional work 
> that GROMACS tools don't do.  You need to analyze water H-bonds with 
> the two groups of interest separately, then determine if the same 
> water is H-bonded to a moiety in both of those groups in the same 
> frame.  This is where tracing the H-bonds in the .xpm file is useful.
> -Justin

Thanks for your comments, Justin.  When I invoke hbond by:

gmx hbond -f *.xtc -s *.tpr -num -hbn -g (± other options)

I get hbnum which shows changes with respect with time, but the 
hbond.ndx and hbond.log files have no time information.  Are they 
averages of some sort?  Or a particular frame that it defaults to? If 
so, how do I specific the frames/times?

Thanks again,

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