Yes I tried the command you wrote but it is still in the corner of the box. Is there anything else I can do? The coordinates I used to center the protein are the ones which are in the last line of the .gro file.
Thank you > > > On 7/11/12 7:12 AM, [email protected] wrote: >> 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? >> > > Have you tried trjconv -pbc mol -ur compact? The "center" of an infinite > system > is an arbitrary location; you have to re-wrap the unit cell to achieve the > expected outcome. It's centered, it just may not look like it in the > current > representation. > > -Justin > >>> >>> >>> On 7/11/12 6:13 AM, [email protected] 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 [email protected] >>> 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 [email protected]. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> > > -- > ======================================== > > 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 [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
