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

Ben Tam btam125 at hotmail.co.uk
Mon Feb 5 17:57:17 CET 2018

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 :


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,

PhD Student

More information about the gromacs.org_gmx-users mailing list