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