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,
Gregory
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