[gmx-users] Ions drifting
jani vinod
genomejani at gmail.com
Thu Dec 18 05:47:25 CET 2014
Dear Johnny,
I want to make the Na or Cl- ion always stay with the protein.
I tried -pbc mol option ans selecting group as Protein_ion but it didn't
work.
Thanks
Vinod
On Thu, Dec 18, 2014 at 9:53 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
>
> Or does the pbc option make everything stay in box?
>
> Like [==] becomes [x=]= and then pbc makes it go back to [==]
>
> where [, ] is the box, x is empty space, and = is water.
>
> I use -pbc mol every time, so far.
>
>
>
>
> On Wed, Dec 17, 2014 at 11:20 PM, Johnny Lu <johnny.lu128 at gmail.com>
> wrote:
> >
> > 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
> >> >
> >> > ==================================================
> >> > --
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