Hi Kavya, > I did use dodecahedron cell. but how does using a dodecahedron cell > be advantageous than any other cell when minimum image violation > has occurred? This is just my inquisitiveness.
In a rectangular cell, such interactions may occur merely by reorientation of the solute. In that case it is likely that self-interactions over PBC have a persistent effect on the dynamics. > And when I was visualizing > the trajectory in VMD along with other periodic images in +/-X, +/-Y and > +/-Z > directions I saw only 26images, this is good for a cubic cell. But how > can I visualize a dodecahedron cell? Which has more faces ---> more periodic > images (If I am not wrong) than a cubic or rectangular cell.. Actually, there are less. A rhombic dodecahedron has 12 neighbours. A cubic/rectangular cell has 6 faces, but for those you also have to consider the neighbours at the edges and corners, which brings the total to 26. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
