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
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
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
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
Hydrogen bonding is approximated by charge-dipole interaction, which is
very orientation-sensitive, the energy of this kind interactions
are proportional to the cosine of the angle.
https://en.wikibooks.org/wiki/Molecular_Simulation/Charge-Dipole_Interactions
On Wed, Jan 15, 2020 at 5:59 PM
