Thanks for the prompt reply Justin, but I'm still not convinced that I can extract the information I seek from the g_hbond program without modification.
I realize this wasn't clear in my initial message: I would like to know how many OH donors are not participating in ANY hydrogen bonds. If I calculate the number of non-hydrogen bound OH donors as the difference between the number of pairs that meet the distance requirement, and the actual number of hydrogen bonds (column 3 minus column 2 in hbnum), then I would be over-counting, as this does not exclude pairs with OH donors that are also included in a hydrogen bond with another O acceptor. Robin Quoting "Robin C. Underwood" <[email protected]>: > > I would like to modify the g_hbond code (or preferably, know how to > implement > g_hbond if it is already capable) to count the number of non-hydrogen bound > water OH donors in a simulation. I define a non-hydrogen bound donor as one > that > does not meet the distance requirement, or one that may meet the distance > requirement for a hydrogen bond, but does not meet the angle requirement. > > An inferred value of non-hydrogen bound OH donors is not exact because there > is > not a rigorously defined maximum value for the number of hydrogen bonds per > water, (e.g. a single OH donor may qualify as part of a hydrogen bond at two > adjacent water's O-acceptor sites, making the maximum possible number of > hydrogen bonds for the water of this particular OH donor greater than 4). > > Is there a way to implement g_hbond to do this? If not, any specific > information > on what to consider, and how to modify the g_hbond source code to count > non-hydrogen bound water OH donors is greatly appreciated. > > Robin > > > -- > Robin C. Underwood > Chemistry Department > 560 Oval Drive > West Lafayette, IN 47907 -- Robin C. Underwood Chemistry Department 560 Oval Drive West Lafayette, IN 47907 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
