[gmx-users] Bond interaction exclusions

[Mark Abraham]

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.

Mark


>
> Please let me know,
>
> thank you.
>
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