[gmx-users] Bond interaction exclusions

XAvier Periole x.periole at rug.nl
Sun Feb 2 18:25:32 CET 2014


The first line "eth    1" tells it all. In that molecule all non-bonded interactions between first bonded neighbors will be excluded. 

Thus the 1-3, 1-4 (and so on) non-bonded interactions will be included. You may add additional exclusions in the [ exclusion ] section of your topology. 

I am not sure what you mean with 1-4 bonded interactions but if you mean non-bonded then see above. 

> On Feb 2, 2014, at 17:29, Xu Dong Huang <xudonghmath at gmail.com> wrote:
> Dear all,
> I am unclear about the bond exclusion properties within gromacs. Using a martini model system, what is the default behavior of setting 
> [moleculetype]
> ;name    exclusions
> eth      1
> exclusions to 1? How do I find out what kind of interaction it is excluding? I am interested in finding out if this is excluding 1-3 interaction or 1-4 interaction. I guess what I also want to know is if my settings are including 1-4 bonded interactions or using only 1-3. 
> Please let me know,
> thank you. 
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