[gmx-users] Optimum slice size (-sl)

[Ashutosh Akshay Shah]

50 slices corresponds to a slice size slightly smaller than the smallest
ions' diameter.

On Sat, Feb 13, 2016 at 4:40 PM, Ashutosh Akshay Shah <ashah at aggies.ncat.edu
> wrote:

> Thank you Andre and Warren!
>
> A note about PME-
> The basic principle is that a system of particles is converted into a grid
> (or "mesh") of density values. The potential is then solved for this
> density grid, and forces are applied to each particle based on what cell it
> is in, and where in the cell it lies. - from wikipedia
>
> This is a graph of potential across a box that I am simulating, using
> different number of slices. I have used the PME method in all cases. The
> minimum ion diameter is 0.25 nm. Note that my box is 12 nm in z-direction,
> but only the 3 to 9 nm portion is of significance (rest is vacuum).
>
> http://s21.postimg.org/s75ck7tdj/potentialslicescomparison.png
>
> The graph shows that more the slice size, better the resolution, even for
> PME. (no visible noise at higher slice numbers)
>
> What should I conclude out of this? Higher the number of slices, better?
> Even using PME?
>
> Ashutosh Shah
> Joint School of Nanoscience and Nanoengineering
>
>
>
>
> On Sat, Feb 13, 2016 at 1:56 PM, Warren Gallin <wgallin at ualberta.ca>
> wrote:
>
>> If you are using a slice and PME, then wouldn’t the slice have to be
>> thick enough to avoid any ion interacting with its own image in adjacent
>> slices?
>>
>> It seems to me that thickness would have to be greater than the ionic
>> radius at the very least.
>>
>> Warren Gallin
>>
>> > On Feb 13, 2016, at 8:39 AM, André Farias de Moura <moura at ufscar.br>
>> wrote:
>> >
>> > the ions may have a radius, but they are distributed continuously along
>> the
>> > system, so you may use slice thicknesses smaller than the ionic radius
>> > you're interested in.
>> >
>> > if the simulation was made on some sort of lattice system (which was
>> very
>> > common back in the 1990's), then the shortest, physically meaningful
>> slice
>> > thickness would be the lattice width. For simulations with freely-moving
>> > species, you should only mind about precision: if thickness is too
>> small,
>> > density profiles may become too noisy, if it is too large you have loose
>> > details of the density profile (maxima, minima, etc), so it's a matter
>> or
>> > trial and error to find out what slice thickness suites you better.
>> >
>> > I hope it helps
>> >
>> > Andre
>> >
>> >
>> > On Sat, Feb 13, 2016 at 11:57 AM, Ashutosh Akshay Shah <
>> > ashah at aggies.ncat.edu> wrote:
>> >
>> >> Hello GROMACS users,
>> >>
>> >> What is the optimum slice size when trying to capture as much
>> variation as
>> >> possible?
>> >>
>> >> Consider a box with an electrolyte having anions and cations
>> distributed in
>> >> it.
>> >>
>> >>
>> >> *Would be accurate to specify a slice size smaller than the diameter
>> of the
>> >> ions while calculating the charge variation across the box?*
>> >> Thanks!
>> >>
>> >> Ashutosh Shah
>> >> Joint School of Nanoscience and Nanoengineering
>> >> --
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>> >
>> >
>> >
>> > --
>> > _____________
>> >
>> > Prof. Dr. André Farias de Moura
>> > Department of Chemistry
>> > Federal University of São Carlos
>> > São Carlos - Brazil
>> > phone: +55-16-3351-8090
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