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 <leilasal...@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 > -- > 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. -- 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.
