[gmx-users] Ions drifting

[jani vinod]

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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