Dear users, If H-D-A angle is 30 degrees (for a case D-H distance is 1.0 A and D-A distance is 3.3 A) then the angle D-H-A is 138.3915 degrees.
D-A distance: 3.3 Angstroms and H-D-A angle: 30 degrees are generous criteria to identify most hydrogen bonds. It seems many people use them too. On Thu, Jan 16, 2020 at 8:20 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/15/20 10:05 PM, Myunggi Yi wrote: > > Dear Dr. Justin Lemkul, > > > > Can you explain why the D-H-A is 150? > > > > If H-D-A is 30, then D-H-A should be smaller than 150 degrees. > > Since the sum of interior angles of a triangle should be 180 degrees... > > See the following triangle. > > > > H > > > > D A > > > > > > Am I missing something? > > > > It's a deviation from linearity. An ideal hydrogen bond has a D-H-A > angle of 180, thus H-D-A of 0. So the 30 degree values specified in > GROMACS is effectively the deviation from linearity rather than being > the complement of this value, which other software uses. > > -Justin > > > On Thu, Jan 16, 2020 at 2:30 AM Justin Lemkul <jalem...@vt.edu> wrote: > > > >> > >> On 1/15/20 11:57 AM, Pandya, Akash wrote: > >>> Hi all, > >>> > >>> I wanted to ask a couple of questions about the hydrogen bonding > >> calculation in Gromacs. > >>> > >>> 1. Why is the default angle cutoff 30 degrees? The reason I ask > >> this is because I’ve seen in other packages with higher angle cutoffs. > >> > >> It depends on how the software defines the angle. The GROMACS convention > >> is the angle corresponds to H-D-A rather than D-H-A like some other > >> programs. H-D-A cutoff of 30 degrees is equivalent to the "conventional" > >> 150-degree D-H-A cutoff. > >> > >>> 2. What’s the best way to define cutoffs for my system? I know > this > >> is ambiguous, but is there a procedure I can use to decide? > >> > >> The default criteria are widely used and usually don't require any > tuning. > >> > >> -Justin > >> > >> -- > >> ================================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalem...@vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> ================================================== > >> > >> -- > >> 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. > >> > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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. -- 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.