[gmx-users] Ewald summation in 2 dimensions with correction

[Dan Gil]

Hi,

I am using gmx potential to measure the electric field. I've reported the
values from field.xvg in my previous email. The field at the edges of the
ionic liquid near the walls will oscillate because of the electric double
layer but it is the bulk field I am concerned with.

I read the supporting information - I thought that the Ewald summation
correction for 2 dimensions was supposed to cancel out interactions between
periodic images in the z direction?

Were you using the regular 3-D Ewald summation in this work? I might try
carrying out the calculations that way.

Dan

On Mon, Nov 13, 2017 at 2:23 AM, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> On 11/11/17 16:44, Dan Gil wrote:
>
>> Hi,
>>
>> Just wanted to see if anyone had any thoughts...
>>
>> For more information, if I use:
>> wall-ewald-zfac = 3
>> E-z                    = 1 5 0
>> The electric field from ionic liquid has a magnitude of 7.5 V/nm in the
>> opposite direction to the applied electric field. This makes no sense to
>> me
>> at all.
>>
>> With
>> wall-ewald-zfac = 5
>> E-z                    = 1 5 0
>> The ionic liquid E is -6.2
>>
> How do you measure the electric field? Using gmx potential?
> What numbers does the (optional?) file field.xvg contain?
>
> There can of course be a difference between applied field and effective
> field, in particular with PBC. I sugges you read the supporting information
> for our paper: Carl Caleman and David van der Spoel: Picosecond Melting of
> Ice by an Infrared Laser Pulse - A Simulation Study Angew. Chem. Intl. Ed.
> 47 pp. 1417-1420 (2008)
>
>>
>> With
>> wall-ewald-zfac = 10
>> E-z                    = 1 5 0
>> The electric field is still slightly above the expected 5 V/nm.
>>
>> The dimensions of the box is about 5x5x20 nm3.
>>
>> Reading various sources say that the wall factor should not matter as long
>> as it is sufficiently large (x3) but in my case it seems to matter a lot.
>> Should I report this as a bug or do you think I can investigate this
>> further?
>>
>> Best Regards,
>>
>> Dan
>>
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>> source=link&utm_campaign=sig-email&utm_content=webmail>
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>>
>>
>> On Wed, Nov 8, 2017 at 11:37 AM, Dan Gil <dan.gil9973 at gmail.com> wrote:
>>
>> Hello,
>>>
>>> I am studying room-temperature ionic liquids in slab geometry and I am
>>> experiencing that I cannot get rid of the interactions between periodic
>>> images in the z-direction. Is there something wrong with what I am doing
>>> or
>>> is this inevitable?
>>>
>>> The reason I think this is because when I change "wall-ewald-zfac" the
>>> results change also.
>>>
>>> Gromacs 5.1
>>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>>> ;Integration Method and Parameters
>>> integrator               = md
>>> nsteps                   = 4000000
>>> dt            = 0.002
>>> nstenergy                = 100
>>> nstcalcenergy            = 100
>>> nstlog                   = 5000
>>>
>>> ;Output Control
>>> nstxout = 100
>>> nstvout = 10000000
>>>
>>> ;Cutoff Schemes
>>> cutoff-scheme            = verlet
>>> rlist                    = 1.0
>>> vdw-type                 = cut-off
>>> rvdw                     = 1.0
>>> DispCorr                 = EnerPres
>>>
>>> ;Coulomb interactions
>>> coulombtype              = pme
>>> rcoulomb                 = 1.0
>>> fourierspacing           = 0.4
>>>
>>> ;Constraints
>>> constraints              = all-bonds
>>>
>>> ;Temperature coupling
>>> gen-vel                  = yes
>>> tcoupl                   = v-rescale
>>> tc-grps                  = System
>>> tau-t                    = 0
>>> ref-t                    = 300
>>>
>>> ;Walls
>>> pbc                      = xy
>>> nwall                    = 2
>>> wall-type                = 10-4
>>> ewald-geometry           = 3dc
>>> wall-atomtype            = cp cm
>>> wall-density             = 5 5
>>> wall-ewald-zfac          = 10
>>>
>>> ;Electric Field
>>> ;Cosine with freq=0, Field V/nm, Phase=n/a
>>> E-z                      = 1 0 0
>>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>>>
>>> Best Regards,
>>>
>>> Dan
>>>
>>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
> --
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