[gmx-users] User-defined Nonbonded Potentials and Cutoff Treatment

[Phillip Rauscher]

Hello all,

I'm trying to systematically scale down the non-bonded interaction between
two specific atom types without perturbing the interactions with the other
species (basically multiplying their pair potential by 0<f<1).  From what I
gather, the most robust method of doing this is to define energy groups for
the two atom types and introduce tabulated potentials for their
interactions.

Normally, I would set "vdw-type = Cutoff", which shifts the potentials as
U(r) - U(rcut) so that the energies are the integrals of the forces.  When
I set "vdw-type = User" how are the cutoffs handled by Gromacs?  As a
related question, how are the tail-corrections handled in this scenario?
If I want the same cut-off and correction behavior as before, how should
the tables be constructed?  Should I define the values as U(r)-U(rcut)? If
so, should the values above my cutoff be set to zero?

I'm only concerned about the vdW behavior here, since I plan on using the
"PME-User" option for the electrostatics (although I'll also be scaling
that interaction similarly via the table).

Finally, if there's an easier way to accomplish this that I'm missing,
please feel free to let me know!

Thanks in advance for your help.

-Phil Rauscher

-- 
Phil Rauscher
Graduate Student
de Pablo and Rowan Research Groups
Institute for Molecular Engineering
University of Chicago