On 12/1/2016 7:45 AM, Justin Lemkul wrote:
On 12/1/16 7:24 AM, Gregory Man Kai Poon wrote:
I am trying to use hbond in Gromacs 5.1.4 to analyze water-mediated
bonding between two objects simulated in water. The GROMACS manual
this in a Figure (9.8) - "water insertion". There is nothing in the
documentation as to how this should be done except a single mention
-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
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
Am I using the correct hbond option to enumerate water-mediated hydrogen
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.
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?
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.