[gmx-users] Dodecahedron Box size and Appropriate number of SOL molecules

[Tsjerk Wassenaar]

Hi Apramita,

No restrictions. You're in charge. To get a correct density, you'll need to
equilibrate with pressure coupling.

Cheers,

Tsjerk



On Tue, Jun 7, 2016 at 1:08 PM, Apramita Chand <apramita.chand at gmail.com>
wrote:

> Hey,
>  Thanks a lot Tsjerk for your advice regarding box size. You've mentioned
> that we could take a box size which lets us add a bit more water than
> needed and we could delete some molecules. So can I use genbox to add water
> and then delete any number of water molecules to reach my target solvent
> number? I'm using a box size of say 2.9 and I want a box of peptide,5 urea
> and 494 water molecules. genbox adds 566 water molecules. Do I have to
> simply delete the extra water molecules and that would be okay after
> equilibration?
> So there is basically no restriction that only a fixed  number of water
> molecules  should be present in a particular box,right?
>
>
> Regards,
> Apramita Chand
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-- 
Tsjerk A. Wassenaar, Ph.D.