[gmx-users] Ewald summation in 2 dimensions with correction
Dan Gil
dan.gil9973 at gmail.com
Wed Nov 15 16:29:12 CET 2017
Hi,
I tried using the regular PME method with and without corrections. The
results don't depend on the choice of ewald-geometry at all!
I used (Gromacs 5.1):
wall-ewald-zfac = 3
ewald-geometry = 3d ; This prompts a warning because I am using 2 walls
- 2d system. I forced this with maxwarn.
E-z = 1 5 0
and I also used
wall-ewald-zfac = 3
ewald-geometry = 3dc ; No warnings since this is recommended
E-z = 1 5 0
I checked that this input was being processing correctly on topol.tpr. For
the first case, I see ewald-geometry = 0 and the second case ewald-geometry
= 1.
The electric field from ionic liquid has a magnitude of ~7.5 V/nm in the
opposite direction to the applied electric field for both cases. This is
greater than the applied 5. I obtained the electric field using gmx
potential.
I would very much appreciate any recommendations.
Dan
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On Mon, Nov 13, 2017 at 10:22 AM, Dan Gil <dan.gil9973 at gmail.com> wrote:
> 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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>>>
>>>
>>> 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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