On 12/1/16 7:24 AM, Gregory Man Kai Poon wrote:
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.
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 files? 2) Am I using the correct hbond option to enumerate water-mediated hydrogen bonds?
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.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.