The donors are two H atoms from the amide group of Gln residues. Thus, I will try the -merge option. Thank for the comment.
I wonder if the following issue is affecting gromacs 4.5.5: http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html 2013/1/11, Justin Lemkul <[email protected]>: > > > On 1/11/13 6:23 AM, Miguel Ángel Mompeán García wrote: >> Hi all, >> >> When calculating the average number of hbonds during a simulation, does >> the >> program g_hbond contemplate the possibility of an atom involved in two >> hbond? >> If I visualize the structures with molden, setting the same cutoff >> criterion for hbonding than g_hbond utilizes, I found out that some O >> atoms >> are forming two H bonds with two different hydrogen atoms at once. Other >> O >> atoms are forming just one H bond. >> >> With g_hbond I get the same average on systems when the same O atoms are >> forming two hbonds and in those where they form just one. >> >> If the criterion is just a cutoff distance and angle, I guess I should >> have >> seen the differences when using g_hbond with -num, but this never >> happened... Any clue? >> > > For O atoms with two putative H-bonds, are the donors on separate functional > > groups or molecules? If they are not, g_hbond considers them the same, > since > that is the default behavior of the -merge option. If you specify -nomerge, > > then the two hydrogen bonds will be considered distinct. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 > -- 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
