Hey Thomas, The rhombic dodecahedron corresponds to the packing of a sphere. Consequently, the difference in the distance between periodic images over the shortest diameter and the longest diameter is pretty small. That means that there isn't really an optimal orientation in a rhombic dodecahedron; all orientations are pretty much equal. And that's how it should be :)
Cheers, Tsjerk On Thu, Apr 26, 2012 at 1:18 PM, Thomas Evangelidis <teva...@gmail.com> wrote: > Dear GROMACS users, > > I have noticed that for constant box dimensions the minimum distance from > the periodic images of a protein depends on the initial orientation of the > protein, whereas the orientation of the dodecahedron relative to the x,y,z > axes remains fixed. These are the command lines I use: > > pdb2gmx_d4.5.5 -f protein.pdb -o protein.gro -p protein.top -ff > amber99sb-ildn -water tip3p -ignh > # set the new dodecahedron box dimensions > editconf_d4.5.5 -f protein.gro -bt dodecahedron -box 13 -o protein_box.gro > # solvate with TIP3P > genbox_d4.5.5 -cp protein_box.gro -cs spc216.gro -o protein_box_solv.gro -p > protein.top > # add ions > grompp_d4.5.5 -f em_real.mdp -c protein_box_solv.gro -p protein.top -o > protein_ions.tpr > echo 13 | genion_d4.5.5 -s protein_ions.tpr -o protein_EM.gro -p protein.top > -pname NA -nname CL -np 3 > > grompp_d4.5.5 -f em_real.mdp -c protein_EM.gro -p protein.top -o > protein_EM.tpr > mpirun -np 2 mdrun_d4.5.5 -v -deffnm protein_EM > > # to see a dodecahedron > echo 0 | trjconv_d4.5.5 -pbc mol -ur compact -f protein_EM.trr -s > protein_EM.tpr -o em_dodecahedron.xtc > # measure the minimum distance from the periodic images > echo 1 | g_mindist_d4.5.5 -f em_dodecahedron.xtc -s protein_EM.gro -pi > > > Is there any way to optimize the orientation of protein inside the > dodecahedron in order to get the maximum possible mindist? > > > Thanks in advance, > Thomas > > > > -- > > ====================================================================== > > Thomas Evangelidis > > PhD student > > Biomedical Research Foundation, Academy of Athens > > 4 Soranou Ephessiou , 115 27 Athens, Greece > > email: tev...@bioacademy.gr > > teva...@gmail.com > > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > > > > -- > 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 -- 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