[gmx-users] (no subject)

[Gregory Man Kai Poon]

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.


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?


Many thanks in advance,

Gregory


https://www.dropbox.com/s/2vj2mxmb0f0jnyq/hbmap.xpm?dl=0


https://www.dropbox.com/s/w0gb4x0frwwm668/plot.eps?dl=0

[https://www.dropbox.com/temp_thumb_from_token/s/w0gb4x0frwwm668?preserve_transparency=False&size_mode=2&size=1024x1024]<https://www.dropbox.com/s/w0gb4x0frwwm668/plot.eps?dl=0>

plot.eps<https://www.dropbox.com/s/w0gb4x0frwwm668/plot.eps?dl=0>
www.dropbox.com
Shared with Dropbox



[https://cf.dropboxstatic.com/static/images/icons128/page_white.png]<https://www.dropbox.com/s/2vj2mxmb0f0jnyq/hbmap.xpm?dl=0>

hbmap.xpm<https://www.dropbox.com/s/2vj2mxmb0f0jnyq/hbmap.xpm?dl=0>
www.dropbox.com
Shared with Dropbox