VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Nov 25 2015 - 11:35:39 CST

On Tue, Nov 24, 2015 at 11:55 PM, sunyeping <sunyeping_at_aliyun.com> wrote:
> But in NAMD Energy plugin of VMD, the interaction potential is the sum of
> vdw and electrostatic potential instead of LJ potential. How are the
> replusion or attraction defined for the electrostatic potential and the
> total interaction potential. Can positive or negative values of these items
> be related to LJ potential?

it looks like you have to retake some introductory classes in physics and math.

the situation is very simple: whether something is attractive or
repulsive does *not* depend on the value of the potential energy, but
on whether it increases or decreases in that direction. that is it.

axel.

> Best regards.
>
> Yeping
>
> ------------------------------------------------------------------
> From:Maxim Belkin <mbelkin_at_ks.uiuc.edu>
> Time:2015 Nov 24 (Tue) 23:48
> To:孙业平 <sunyeping_at_aliyun.com>
> Cc:vmd-l <vmd-l_at_ks.uiuc.edu>
> Subject:Re: vmd-l: Attractive or repulsive with Namd Energy?
>
> The region is ro < r < re: potential is negative, species repel.
>
>
>
> On Nov 24, 2015, at 02:43, sunyeping <sunyeping_at_aliyun.com> wrote:
>
> Hi Maxim,
>
> Please see the attached figure. It shows that positive energy is replusive
> while nagetive energy is attractive. Where is the second "region" you listed
> in which LJ potential is negative and the species repel each other?
>
> All the best.
>
> Yeping
>
> ------------------------------------------------------------------
> From:Maxim Belkin <mbelkin_at_ks.uiuc.edu>
> Time:2015 Nov 24 (Tue) 03:12
> To:孙业平 <sunyeping_at_aliyun.com>
> Cc:vmd-l <vmd-l_at_ks.uiuc.edu>
> Subject:Re: vmd-l: Attractive or repulsive with Namd Energy?
>
> 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> 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
>
>
>
>
>
> <Lennard-Jones potential.jpg>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.