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: [email protected] [email protected] website: https://sites.google.com/site/thomasevangelidishomepage/
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
