[gmx-users] size of the box for peptide

[Dr. Vitaly Chaban]

the layer of water must be thicker than the interaction cut-off.




Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Mon, Nov 3, 2014 at 8:44 PM, leila salimi <leilasalimi at gmail.com> wrote:
> Dear gromacs users,
>
> I want to simulate the conformation of peptide in solution (20 monomers of
> Glutamate with solution). I am in doubt about the size of the box, and
> number of water molecules.
> I want to consider rhombic dodecahedron box. For example I chose a box with
> approximately 498 nm^3 that contain 16369 water molecules.
> I did NVT and NPT equilbiration and I checked the density and it is fine.
> My question is that how I can chose the smallest cell that also no
> interaction between peptides form neighbouring PBC cell.
>
> As I want to use BP-REMD simulations, it is important to have the efficient
> size of the system without any interaction between polymers.
>
> Thanks very much,
> Leila
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