[gmx-users] Using xy periodic boundary and 3dc Ewald summation
btam125 at hotmail.co.uk
Thu Feb 8 15:43:49 CET 2018
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?
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
>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.
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 :
> 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
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users