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

[Ben Tam]

Hi Dan,

Thank you for your answer. If gromacs' pbc =xy still calculate periodic in the z-direction, how does gromacs take care of the z-direction Ewald?

Best regards,

Ben
________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Dan Gil <dan.gil9973 at gmail.com>
Sent: Tuesday, February 6, 2018 03:49
To: gmx-users at gromacs.org
Cc: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] Using xy periodic boundary and 3dc Ewald summation

I believe that the 3DC method still applies summations over Z. From the
abstract of the paper: "The proposed method adds a correction term to the
standard Ewald summation formula."

What the 3DC method does is add a correction term so that unrealistic
electrostatic interactions between periodic images in the Z direction is
cancelled.

>From what I understand, Gromacs' pbc=xy is still periodic in the
z-direction, hence the zfac option.

Please use Gromacs 2016.4 version and newer, since the devs fixed a bug
associated with the 3DC method and PME.

Dan

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On Mon, Feb 5, 2018 at 11:57 AM, Ben Tam <btam125 at hotmail.co.uk> wrote:

> 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
>
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