VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon Feb 25 2019 - 07:47:05 CST

Dear Ernest,
If you use only a single atom group, the pairinteractions implementation in
namd will give energies for all bonded interactions that *involve* the
selected atom, so with your atom selection, you're not just singling out
the two bonds and one angle contained in your selection, but also the other
bonds and angles that they are involved in. If you're interested in
literally only calculating those precise bonds and angle, you might be
better off just recording the coordinates and directly calculating the
energy based on the force field that you are using.
Best,
Peter

On Mon, Feb 25, 2019 at 7:06 AM Ern Ong <Ern.Ong_at_student.adfa.edu.au> wrote:

> 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
>