[gmx-users] Ions drifting

[Johnny Lu]

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 <genomejani at 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 <jalemkul at 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
> >
> > jalemkul at 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-request at 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-request at gromacs.org.
>