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.
