[gmx-users] tabulated potentials - cutoff

[Sabine Reisser]

Hi,

I'm using tabulated potentials to create a hole in a membrane. I define 
three groups: 2 dummy-atoms, all hydrophobic lipid chains, and rest. For 
the interactions between the dummy atoms and the hydrophobic chains I 
define an exclusively repulsive potential. All other interactions are 
defined normally (Coulomb, 6-12 LJ potentials). The 2 dummy atoms are 
placed on top and below the lipid bilayer, directly over each other. 
Then I use the pull code to pull the two dummy-atoms towards each other, 
thereby repelling the hydrophobic lipid chains and opening a pore.

This works. But I couldn't figure out how the long range interactions 
are treated. I assumed only interactions are counted where the distance 
between atoms is within the range defined in my tables. However, I do 
define a cutoff radius max(rcoulomb, rvdw), I will call it rcutoff now. 
In the tables, I have to define values up to rcutoff+1.
Is this cutoff radius only to tell GROMACS to expect values up to 
rcutoff+1? So everything until rcutoff+1 is calculated explicitly after 
the tables and everything beyond is ignored?

I'm asking because usually membranes are quite sensitive to these cutoff 
values. I would assume that I would see clear changes in e.g. the area 
per lipid if I simulated long enough.

Cheers
Sabine