From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Mon Nov 23 2015 - 13:11:33 CST

Hi Yeping,

I agree with Jerome, but I’ll expand a little bit.

tl;dr answer: negative force means species are attracting; positive force - repelling each other.

Longer answer:
Technically speaking, absolute value of energy without some reference value (level) is meaningless.
The Lennard-Jones potential, however, has a reference value: potential value at r = infinity (potential value is 0). If you look closely at the LJ curve, you should see three "regions" where:

1. LJ potential is positive and the species repel each other.
2. LJ potential is negative and the species repel each other.
3. LJ potential is negative and the species attract each other.

Because of the third Newton’s law, it makes sense to talk about force magnitude only in the common center of mass reference frame and spherical coordinates. In such a reference frame and coordinate system, positive magnitude of a vector means it points AWAY from the center of mass. Therefore, negative force means species are attracting, while positive force - repelling each other.

Hope this helps,

Maxim

> On Nov 23, 2015, at 03:33, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
>
> 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 <mailto: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/ <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
>
>
>