VMD-L Mailing List

From: sunyeping (sunyeping_at_aliyun.com)
Date: Sun Nov 22 2015 - 20:15:06 CST

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