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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
