[gmx-users] g_hbond existence matrix

Justin Lemkul jalemkul at vt.edu
Thu Jan 24 20:10:32 CET 2013

On 1/24/13 11:03 AM, Kavyashree M wrote:
> Dear users,
> I have a little confusion -
> The hbmap.xpm file gives the existence of each hydrogen bond.
> The file mentions -
> "   c #FFFFFF " /* "None" */,
> "o  c #FF0000 " /* "Present" */,
> Meaning -
> character "<space>" in white colour means Hbond not present
> character "o" in red colour means Hbond is present.
> In addition, the file also contains white coloured "o" what is
> this?

There are only two characters in the .xpm file, a space and an 'o' as you noted 
above.  The font color that appears in your terminal is whatever you have set it 
to be; there is no significance of different colored letters in the .xpm file. 
There either is a hydrogen bond in a frame (in which case you see 'o') or there 
is not (and thus a blank space).



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list