Re: [gmx-users] Ordering of hydrogen bonds in -hbn and -hbm output in g_hbond

Hi, I think the confusion arises from how the xpm data is displayed. If you have the hb-index on the y-axis in a plot with the positive y-direction pointing upwards (as in most plots), then the first line in the xpm file is actually displayed at the bottom. For matrices, however, the indexing s

Re: [gmx-users] Ordering of hydrogen bonds in -hbn and -hbm output in g_hbond

I think the confusion arises form 15 aug 2012 kl. 22.53 skrev Justin Lemkul: > > > On 8/15/12 4:49 PM, Andrew DeYoung wrote: >> Hi, >> >> I am a novice user of g_hbond (actually, I am using double precision -- >> g_hbond_d -- but I think all of the parameters should be the same). >> >> I woul

Re: [gmx-users] Ordering of hydrogen bonds in -hbn and -hbm output in g_hbond

On 8/15/12 4:49 PM, Andrew DeYoung wrote: Hi, I am a novice user of g_hbond (actually, I am using double precision -- g_hbond_d -- but I think all of the parameters should be the same). I would like to use the output of the -hbn switch (which generates hbond.ndx) in tandem with the -hbm switc

[gmx-users] Ordering of hydrogen bonds in -hbn and -hbm output in g_hbond

Hi, I am a novice user of g_hbond (actually, I am using double precision -- g_hbond_d -- but I think all of the parameters should be the same). I would like to use the output of the -hbn switch (which generates hbond.ndx) in tandem with the -hbm switch (which generates an existence matrix hbmap.x