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

feng chen fch6699 at yahoo.com
Fri Apr 3 22:57:37 CEST 2009

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!


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