Hi Justin, ah okey. Thank you. And I have another question. Why is the protein in the corner of the box and not in the middle? I thought I centered it with the command:
editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470 5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut Or not? > > > On 7/11/12 6:13 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi everybody, >> I did a minimization of my structure. But the output seems a bit strange >> for me, since my input was the protein with its membrane in a box like >> this: >> # = box P = Protein M=Membrane >> >> >> ############# >> # PPPP # >> # MPPPPM# >> # PPPP # >> # # >> # # >> ############# >> >> But the output of the minimization looks like this >> >> ############# >> # PPPP# >> #M MPPPP # >> # PPPP # >> # # >> # # >> ############## >> >> How can that be? > > It's a triclinic representation of the unit cell. Nothing is wrong. > >> My box was created with: >> >> editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470 >> 5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut >> > > Is a dodecahedral box appropriate for a protein in a membrane? The > inherent > symmetry of a slab of any sort dictates that you should be using a cubic > or > rectangular box. Dodecahedral and octahedral boxes are better for systems > with > spherical symmetry, like globular proteins in water. > >> >> I put solvent in it with: >> >> genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro >> 2>>logErr 1>>logOut >> >> >> The mdp file for the minimization looks like this: >> >> define = -DPOSRES >> integrator = steep >> emtol = 10 >> nsteps = 1500 >> nstenergy = 1 >> energygrps = System >> coulombtype = PME >> rcoulomb = 0.9 >> rvdw = 0.9 >> rlist = 0.9 >> fourierspacing = 0.12 >> pme_order = 4 >> ewald_rtol = 1e-5 >> pbc = xyz >> >> >> Can you please tell me how I can prevent my box to shift? >> > > There is no box shift; it's just a visual representation of the > dodecahedral > box. You can "correct" it (for visualization purposes) by running trjconv > -pbc > mol -ur compact. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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