[gmx-users] Bond interaction exclusions

[XAvier Periole]

Hi, 

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. 
> 
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.