[gmx-users] Bond interaction exclusions

Mark Abraham mark.j.abraham at gmail.com
Sun Feb 2 18:39:07 CET 2014

On Sun, Feb 2, 2014 at 5:29 PM, 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?

The others have covered this one

> How do I find out what kind of interaction it is excluding?

grompp will produce slightly different output to the terminal, but this is
not really what you want.

> 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.

Only by inspecting the contents of the .tpr can you really know what is
going on. You can compare two .tpr files with gmxcheck, but for your own
sanity, I would construct a very simple input file (e.g. ethane) before
attempting this.


> Please let me know,
> thank you.
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