[gmx-users] Help on Exclusions and 1-4 Interactions

Mark Abraham Mark.Abraham at anu.edu.au
Fri Apr 3 23:45:32 CEST 2009

feng chen wrote:
> Dear all,
>   Recently,We have tried to implement our own version of frce felds into 
> Gromacs 3.3.3. On the purpose of testing, we dumped out all the 
> infrmation from tpr by using gmxdump. Everything goes fine except this 
> 1-4 interactions terms. The prblem we had is that even though we had set 
> number of exclusion to 3 in our itp files, but still got all 1-4 pairs 
> generated(in gmexdump output), together with LJ-14 and Coulomb-14 
> energies( in log fiels). This is confusing, since based on our 
> understanding whenever number of exclusion is 3, any kinda 1-4 
> interaction should be excluded. Thereforce, none of those 1-4 pairs will 
> be generated. Well,apparently, that's not the case here for gromacs. And 
> we have no idea what's happenning here.
>   Any hints or suggestions will be highly appreciated!

Other than reading chapter 5, I can only suggest that you're probably 
adding 1-4 interactions in your [ pairs ] section.


More information about the gromacs.org_gmx-users mailing list