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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
