[gmx-users] Difference between LJ-14 and LJ(SR)

Heng Ma henglamar at yahoo.com
Wed Apr 5 05:34:35 CEST 2017

Hi, all, 
I recently came across the calculation of intramolecular energy using g_energy in gromacs.There were 2 outputs, LJ-14 and LJ(SR) that I found very ambiguous in the explanation on the manual.I want to share my understanding with the community to make sure I have the right result. 1) To my knowledge, LJ-14 is the intramolecular interaction Only between every i and i+3 atoms.  Atom pairs    for LJ-14 are listed in the item of "Pair" of *top file.  2) With the default nrexcl = 3 is used in *top file,  LJ(SR) include intramolecular LJ energy between i and other atoms are more than 3 bonds away, and all intermolecular LJ interactions.  The interactions between i and i+1 or i+2 or i+3 inside a molecule were excluded from LJ(SR) term, for the default nrexcl = 3. And it is the same with Coul-14 and Coul(SR). Pls help me confirm whether my understanding is correct. Let me know if there is anything wrong with my understanding of those terms. 
Thanks a lot. 
Heng Mahma at lamar.eduPhD candidate,Department of Chemical Enginnering,Lamar University, TX. 

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