[gmx-users] Optimum slice size (-sl)
wgallin at ualberta.ca
Sat Feb 13 19:57:03 CET 2016
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.
> 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
> 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
>> Consider a box with an electrolyte having anions and cations distributed in
>> *Would be accurate to specify a slice size smaller than the diameter of the
>> ions while calculating the charge variation across the box?*
>> 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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