Dear Sir Thanks I got the point!
Thanking you With Regards M. Kavyashree On Mon, Jun 27, 2011 at 12:19 PM, Tsjerk Wassenaar <tsje...@gmail.com>wrote: > 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 >
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