Hi Thomas, Apologies, you are right. I was thinking of the distance to the wall. If the protein is elongated, it will matter in the minimal distance whether the protein major radius is oriented towards a face or towards a corner. In addition, the shape of the protein plays a role. Yet it doesn't really matter for the setup of the simulation, since the rhombic dodecahedroon is built according to the radius of the system, added the distance to the wall (-d). The rhombic dodecahedron is constructed based on the inscribed sphere with that radius, such that every orientation will satisfy the minimal distance between images. For a given solute, the rhombic dodecahedron is uniquely defined, regardless the orientation, in contrast to what happens with a rectangular unit cell.
I hope this clarifies things. Cheers, Tsjerk On Thu, Apr 26, 2012 at 3:57 PM, Thomas Evangelidis <teva...@gmail.com> wrote: > Hi Tsjerk and Erik, > > Thanks for the comments. It's strange, because I get different minimum > distance for different orientations of the same protein structure using the > afore-mentioned command lines. I used a single step energy minimization for > speed (em_real.mdp). Below are the outputs of editconf and the last lines of > the output .gro files. There are differences in the Volume (884.007 nm^3 > versus 996.803 nm^3), system size, center, box vectors, box volume, and > shift. What do these differences mean? Can they explain the different > mindist I get? > > ## > ## Protein Orientation 1 editconf_4.5.5 output: > ## > > Read 17463 atoms > Volume: 884.007 nm^3, corresponds to roughly 397800 electrons > No velocities found > system size : 9.205 8.440 11.378 (nm) > diameter : 12.498 (nm) > center : 6.524 6.242 9.385 (nm) > box vectors : 9.205 8.440 11.378 (nm) > box angles : 90.00 90.00 90.00 (degrees) > box volume : 884.01 (nm^3) > shift : 3.226 3.508 -4.789 (nm) > new center : 9.750 9.750 4.596 (nm) > new box vectors : 13.000 13.000 13.000 (nm) > new box angles : 60.00 60.00 90.00 (degrees) > new box volume :1553.51 (nm^3) > > > ## Last line of the output .gro file: > 13.00000 13.00000 9.19239 0.00000 0.00000 0.00000 0.00000 > 6.50000 6.50000 > > ## g_mindist output: > > Last frame 0 time 2.000 > > The shortest periodic distance is 1.5735 (nm) at time 2 (ps), > between atoms 992 and 8506 > > > ## > ## Protein Orientation 2 editconf_4.5.5 output: > ## > > Read 17463 atoms > Volume: 996.803 nm^3, corresponds to roughly 448500 electrons > No velocities found > system size : 12.299 9.828 8.247 (nm) > diameter : 12.498 (nm) > center : 5.898 4.759 8.713 (nm) > box vectors : 12.299 9.828 8.247 (nm) > box angles : 90.00 90.00 90.00 (degrees) > box volume : 996.80 (nm^3) > shift : 3.852 4.991 -4.117 (nm) > new center : 9.750 9.750 4.596 (nm) > new box vectors : 13.000 13.000 13.000 (nm) > new box angles : 60.00 60.00 90.00 (degrees) > new box volume :1553.51 (nm^3) > > ## Last line of the output .gro file: > 13.00000 13.00000 9.19239 0.00000 0.00000 0.00000 0.00000 > 6.50000 6.50000 > > ## g_mindist output: > > Last frame 0 time 2.000 > > The shortest periodic distance is 2.59235 (nm) at time 2 (ps), > between atoms 3915 and 6814 > > > > Thanks in advance, > Thomas > > > > On 26 April 2012 15:36, Tsjerk Wassenaar <tsje...@gmail.com> wrote: >> >> 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
