[gmx-users] size of the box for peptide

leila salimi leilasalimi at gmail.com
Mon Nov 3 18:44:30 CET 2014

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,

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