VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Nov 23 2015 - 03:33:30 CST

Hi,

This is not a VMD (or a NAMD) question. This is a basic math / phys chem
question.

Look at the graph of a Lennard-Jones potential, and you'll see the answer
to your question. If you don't, take a math class.

Jerome

On 23 November 2015 at 03:15, sunyeping <sunyeping_at_aliyun.com> wrote:

> Dear all,
>
> When calculating the interaction energy between two groups of residues
> with Namd Energy Plugin in VMD, I find the the value of the interaction
> energy is negative but that of the force is positve. According to the user
> guide of the Namd Energy plugin (
> http://www.ks.uiuc.edu/Research/vmd/plugins/namdenergy/), a positive
> force is repulsive. But does the negative value of the interaction energy
> suggest a favorable binding? So whether are these two groups of residues
> attractive or repulsive?
>
> Thanks in advance.
>
>
> Yeping Sun
>
> Institute of Microbiology, Chinese Academy of Sciences
>
>