[gmx-users] Ions drifting

[Johnny Lu]

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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