[gmx-users] re: non-bonded interactions in GROMACS

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Sep 12 07:33:53 CEST 2006

>In manual (chapter 4 page no 62) it was written The use of RB potential 
>implies exclusion of LJ interaction between first and the last atom of the 
>dihedral (mean 1-4 interaction).So why I am getting LJ-14 and Coulomb-14 
>energy in my log file (see below) is there is any problem in this 
>simulation or it is normal? 

Only the 1-4 interactions spanning RB potentials should be excluded from LJ-14 
and coulomb-14. For example, lipid headgroups may be treated without RB's and 
the acyl chains treated with RB's. If you want to see where things are coming 
from, make an index file and then use enerygrps in your .mdp so that g_energy 
can give you some useful output for further testing. Look at your [ pairs ] 
section in your .itp file. Those are the source of the LJ-14 and Coulomb-14 

>and what I understood from articles on OPLS force field that it scale down 
>the LJ-14 and Coulomb-14 energy my a factor of two? as it is specify in 
>ffoplsaa.itp file 
>what about GROMOS96 force field, it is mention in manual (Chapter 4 page 
>no 75) it also scale down the LJ-14 repulsion term . 
>what I understood by manual that It uses separate parameter for LJ-14 
>interaction Is it is correct? If yes then It uses separate parameters only 
>for LJ repulsive term or all the non bonded terms i.e.  LJ repulsive,LJ 
>attractive and for coulomb term? 

The .itp file for your molecules will have the information that you are after.
1. The [ pairs ] section is a list that defines what 1-4 interactions exist. If 
a 1-4 pair is not in the [ pairs ] section, LJ-14 and Coulomb-14 interactions 
will not be included in the energies.

**That's a good test for you right there. Remove all entries from the [ pairs ] 
section and your 1-4 energies should drop to zero.

2. The charges for 1-4 interactions are the normal ones, and FudgeQQ will be 
3. The LJ sigma / epsilon parameters will be taken from [ pairs ] if they are 
there, or (second in hiearchy) from [ pairtypes ] if they are there, or (third 
in hiearchy) generated from the regular non-bonded parameters if gen-pairs=yes. 
In this third case, FudgeLJ is applied.

Each force-field has its own rules (e.g. gen-pairs and FudgeLJ/QQ), but these 
apply to the information outlined above. For example, gen-pairs does NOT mean 
"generate a [ pairs ] section for the molecule." Instead, it means "If LJ-14 
epsilon and sigma are not present in a [ pairs ] section entry, and that type of 
interaction is not explicitly formulated in [ pairtypes ], then it is 
permissible to use the regular non-bonded parameters, and in that case scale 
them by FudgeLJ."

OPLS-AA uses gen-pairs=yes, Force-fields that use gen-pairs=no (GROMOS96 I 
think) will have a very large [ pairtypes ] section. FudgeLJ is not used when 
gen-pairs=no, but FudgeQQ is always used. Note that it is perfectly reasonable 
to scale the 1-4 FudgeQQ/LJ and set gen-pairs=no.

If there is still misunderstanding, do a search for {pairs pairtypes}. 

Also, if your main concern is ensuring that you don't have any 1-4 interactions 
where you shouldn't then I would recommend drawing out your molecule and making 
sure that you don't have any RB dihedrals defined with an overlapping entry in 
the [ pairs ] section. However, this is not absolutely going to work because it 
gets complicated sometimes. Eg: I have yet to figure out exactly why things are 
treated as they are in the [ pairs ] section for two non-RB double-bonded 
carbons in the middle of a long chain of RB carbons :: more specifically I am 
referring to lipid acyl chains with a double bond (for example pope.itp from Dr. 


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