AMBER Archive (2005)

Subject: Re: AMBER: box size in explicit water

From: Melinda Layten (mlayten_at_gmail.com)
Date: Wed Jul 06 2005 - 11:52:55 CDT

It depends on the type of simulation you are doing. If you have a restrained
system and our doing short runs, then there is little to no chance that your
system will unfold and interact across the boundary. If you are doing high
temperature unfolding runs, you would need a much bigger box to prevent
interactions.

On 7/6/05, Lwin, ThuZar <ThuZar.Lwin_at_stjude.org> wrote:
>
> Dear Amber users,
> I have a protein that is 50Angstrom in diameter and I would like to
> solvate it.
> So I did
>
> solvateOct protein TIP3PBOX 8
>
> Is 8 angstrom buffer appropriate for my system? In general, how do I know
> what size of buffer to use relative to the size of a protein? The side of
> water box after constant pressure equilibration is 60 angstrom.
>
> Thanks,
> ThuZar
>
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