[gmx-users] Ions drifting

[Justin Lemkul]

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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