[gmx-users] Using xy periodic boundary and 3dc Ewald summation

[Ben Tam]

Dear GROMACS user,

Currently I am simulating a Metal Organic Frameworks membrane, in which I have applied vacuum space at z direction (3 times of the current non-vacuum system). Following the instruction on GROMACS, I have set the pbc = xy and  ewald-geometry = 3dc. So here is my first question, how does GROMACS calculated the electrostatic potential for z direction when pbc = xy? Does it just use Columb's equations?

Then following on with my second question. In this paper :

http://aip.scitation.org/doi/abs/10.1063/1.479595

As far as I understand, 3dc is done by Ewald summation for all xyz direction then a pseudo term is applied to z direction. Then from my understanding is that pbc = xy turn off Ewald summation at z direction, thus how does GROMACS calculated 3dc with z direction periodic boundary turn off (as the pseudo term have to based on full pbc system)?

Thank you very much for your help.

Best regards,

Ben
PhD Student