Re: [gmx-users] how to optimize the orientation of the protein in a dodecahedron
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 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: > 13.0 13.0 9.19239 0.0 0.0 0.0 0.0 > 6.5 6.5 > > ## 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: > 13.0 13.0 9.19239 0.0 0.0 0.0 0.0 > 6.5 6.5 > > ## 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 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 >> 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 e
Re: [gmx-users] how to optimize the orientation of the protein in a dodecahedron
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: 13.0 13.0 9.19239 0.0 0.0 0.0 0.0 6.5 6.5 ## g_mindist output: Last frame 0 time2.000 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: 13.0 13.0 9.19239 0.0 0.0 0.0 0.0 6.5 6.5 ## g_mindist output: Last frame 0 time2.000 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 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 > 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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Maili
Re: [gmx-users] how to optimize the orientation of the protein in a dodecahedron
Hi, And even if not all orientations are exactly equal in this respect, bare in mind that the solute might rotate during the simulation, taking it out of any optimum. Erik 26 apr 2012 kl. 14.36 skrev Tsjerk Wassenaar: > 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 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 listgmx-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 listgmx-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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-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
Re: [gmx-users] how to optimize the orientation of the protein in a dodecahedron
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 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 listgmx-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
[gmx-users] how to optimize the orientation of the protein in a dodecahedron
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 listgmx-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
