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

[Dan Gil]

The details are in the article you linked and it will do a much better job
of explaining it than I can.

Let me clarify what I have said in the previous message: Gromacs is using
the correction described in the paper.

On Thu, Feb 8, 2018 at 9:43 AM, Ben Tam <btam...@hotmail.co.uk> wrote:

> 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-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Dan Gil <
> dan.gil9...@gmail.com>
> Sent: Tuesday, February 6, 2018 03:49
> To: gmx-us...@gromacs.org
> Cc: gromacs.org_gmx-users@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 <btam...@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
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [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-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Dan Gil 
<dan.gil9...@gmail.com>
Sent: Tuesday, February 6, 2018 03:49
To: gmx-us...@gromacs.org
Cc: gromacs.org_gmx-users@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 <btam...@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
>
> --
> 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-requ...@gromacs.org.
>
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Re: [gmx-users] Using xy periodic boundary and 3dc Ewald summation

[Dan Gil]

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  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
>
> --
> 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-requ...@gromacs.org.
>
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