From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Tue May 05 2020 - 18:09:35 CDT
A more concrete perspective: you want at least 30 Angstroms of solvent
between protein copies over the PBC edges in most biological contexts. You
*might* be able to get away with less if your dielectric of the media is
higher, but for water, 30 is about right.
On Tue, May 5, 2020 at 1:55 PM Oscar Bastidas <obastida_at_umn.edu> wrote:
> If you really want to get super quantatative about a size of water box
> that's big enough so your protein doesn't interact with itself, you could
> look at how the Particle Mesh Ewald is calculated and determine a
> reasonable distance where those long distance interactions no longer have
> an influence on each other.
> On May 4, 2020 9:57 PM, "HEMANTH H" <hemanth.h_at_iitgn.ac.in> wrote:
> The normal way would be to ensure that your protein or whatever is the
> system of interest is sufficiently solvated, i.e the molecule doesn't
> interact with it's periodic images.
> On Tue, 5 May 2020, 05:45 L-, <lamyaoo_at_gmail.com> wrote:
>> if i want to solvate my protein in a water box
>> is it 10 or 15 or 20 or 40 Angstroms?
>> Can anyone help me how to calculate (if there is a formula or so) how big
>> the box should be ?
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