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From: sunyeping (sunyeping_at_aliyun.com)
Date: Tue Nov 24 2015 - 22:55:06 CST

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?Best regards.Yeping------------------------------------------------------------------From:Maxim Belkin <mbelkin_at_ks.uiuc.edu>Time:2015 Nov 24 (Tue) 23:48To: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) 03:12To: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,MaximOn 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.JeromeOn 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>