VMD-L Mailing List

From: Ern Ong (Ern.Ong_at_student.adfa.edu.au)
Date: Mon Feb 25 2019 - 04:39:21 CST

Dear VMD users,

I am using VMD for WIN32, version 1.9.3 (November 20, 2016). I want to calculate the bond and angle energy of a glucosidic linkage (C1-O4-C4) and I am using the NAMD Energy plugin to perform the calculation. However, I am not sure whether I did it in a correct way or not. I inserted "name C1 O4 C4" in the Selection 1 and selected "Bonds" and "Angles" to perform the calculation.

To make sure the above calculation is correct, I added up the bond energy calculated by inserting "name C1 O4" and "name C4 O4" in Selection 1 (that were calculated separately). I found that the bond energy calculated using "name C1 O4 C4" is smaller than the total bond energy of "name C1 O4" and "name C4 O4".

Hope that someone can help me on this.

Thank you.

Regards,
Ernest