[gmx-users] Setup Box Size

[Nuno R. L. Ferreira]

From: "Anton Feenstra" <feenstra at chem.vu.nl>
>
> I usually take the distance between protein and box-edge slightly larger
than
> the largest of rvdw or rcoul (which are always equal for me anyway), so
for the
> usual rvdw=rcoul=1.4 for the Gromos 43a1 ff, I use 'editconf -d 0.8 -bt
dode'.
>

So, the answer to my previous question posed to J. Kerrigan is: protein
/protein distance, hence -d > 0.5*("largest of rvdw or rcoul ").
Right?

BTW, why so many people talk about the advantages of using PME, but still
use coulombtype = cuttof?
Time computational cost? Bad scalling in parallel runs?
I assume that rvdw=rcoul=1.4 means that you're doing cutoff for vdw and
coulomb.

Regards,
NUno