Hi. I guess the pbc option only make a previously non-periodic box become periodic.
Do you want to: 1. Make the Na or Cl- ion always stay with the protein. Or 2. Make the protein looks like it stays at the center of the box. (but it can still rotate) I think the protein would look like it stays one piece as well. Or 3. Make the protein looks like it doesn't rotate. May be this post can help: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-December/094369.html On Wed, Dec 17, 2014 at 10:57 PM, jani vinod <genomej...@gmail.com> wrote: > > Dear Justin and Tsjerk, > Thanks for suggestion . It seems to be visualization problem . Since when I > observed gro file generated at the end of simulation appear to be normal > . > I tried various option with pbc (whole followed by nojump) , pbc(mol -ur > compact), pbc (whole , clust , nojump) but none of this seems to be working > in my case. > I followed the gromacs page where they mentioned how to deal pbc problem > but that also didn't help. > So is their any protocol for such system where we want to see interaction > of solvent with solute. > > Thanks and regards > Vinod > > > > On Wed, Dec 17, 2014 at 6:29 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > > On 12/16/14 11:41 PM, jani vinod wrote: > > > >> Thanks > >> following was the mdp file > >> > >> title = Protein in ions > >> ; Run parameters > >> integrator = md ; > >> nsteps = 50000000 ; > >> dt = 0.002 ; > >> ; Output control > >> nstxout = 5000 ; > >> nstvout = 5000 ; > >> nstenergy = 5000 ; > >> nstlog = 5000 ; > >> nstxtcout = 5000 > >> ; > >> ; Bond parameters > >> continuation = yes ; > >> constraint_algorithm = lincs ; > >> constraints = all-bonds ; > >> lincs_iter = 1 ; > >> lincs_order = 4 ; > >> ; Neighborsearching > >> ns_type = grid ; > >> nstlist = 10 ; > >> rcoulomb = 1.0 ; > >> rlist = 1.0 ; > >> rvdw = 1.0 ; > >> ; Electrostatics > >> coulombtype = PME ; > >> pme_order = 4 ; > >> fourierspacing = 0.16 ; > >> ; Temperature coupling is on > >> tcoupl = Nose-Hoover > >> tc-grps = Protein Non_Protein > >> tau_t = 0.5 0.5 ; > >> ref_t = 300 300 ; > >> ; Pressure coupling is on > >> pcoupl = Parrinello-Rahman ; > >> pcoupltype = isotropic ; > >> tau_p = 2.0 ; > >> ref_p = 1.0 ; > >> compressibility = 4.5e-5 ; > >> ; Periodic boundary conditions > >> pbc = xyz ; > >> ; Dispersion correction > >> DispCorr = EnerPres ; > >> ; Velocity generation > >> gen_vel = no ; > >> nstcomm = 1 > >> comm-mode = Linear > >> comm-grps = Protein Non_Protein > >> > >> > > It does not make sense to separate COM motion removal like this for a > > simple protein in water. As to whether or not this is related to the > > problem at hand, I can't necessarily say, but it is artificial. > > > > . So I processed the trajectory with trjconv whole option followed by > >>>> nojump. > >>>> After that the protein appear on one side and ions on other > >>>> > >>> > > So this is all likely a visualization issue. Use trjconv to center the > > protein in the unit cell in conjunction with -pbc mol. > > > > -Justin > > > > -- > > ================================================== > > > > Justin A. Lemkul, Ph.D. > > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > > > Department of Pharmaceutical Sciences > > School of Pharmacy > > Health Sciences Facility II, Room 629 > > University of Maryland, Baltimore > > 20 Penn St. > > Baltimore, MD 21201 > > > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > http://mackerell.umaryland.edu/~jalemkul > > > > ================================================== > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.