[gmx-users] generate pair list and 1-4 interactions

Enemark Soeren chees at nus.edu.sg
Thu Jul 30 09:58:40 CEST 2009

Dear all,

I am a bit confused about how the pair potentials (PPs)are calculated.


If I state explicitly sigma and epsilon values for the pair potentials,
can I then still have a coulomb scaling of my 1-4 interactions?

Say I set "gen-pairs" to "yes", although I have all possible pair
potential interactions specified under "[ pairtypes ]", would I then
still be able to scale my 1-4 coulomb interactions by setting a
"FudgeQQ" different from 1? Also, would I be able to scale the already
given van der Waals interactions with "FudgeLJ"?


Finally, are generated pair potentials based on the parameters specified
under "[ atomtypes ]" or "[ nonbond_params ]" (if the latter exist) in
the ffamber03nb.itp file?


Best regards,

Soren Enemark


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