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

[André Farias de Moura]

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