[gmx-users] Ions drifting

[jani vinod]

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

Regards
Vinod

On Wed, Dec 17, 2014 at 10:05 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
>
> this mail list can't take attachment. probably have to upload this
> somewhere or paste it in the email.
>
> On Tue, Dec 16, 2014 at 11:25 PM, jani vinod <genomejani at gmail.com> wrote:
> >
> > Dear Justin,
> > Thanks for reply
> > I am using following attached mdp file
> > In raw trajectory protein molecule appears to be broken but ions around
> it
> > . So I processed the trajectory with trjconv whole option  followed by
> > nojump.
> > After that the protein appear on one side and ions on other
> >
> > Thanks
> > Vinod
> >
> >
> >
> > On Tue, Dec 16, 2014 at 6:14 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> > >
> > >
> > >
> > > On 12/16/14 1:34 AM, jani vinod wrote:
> > >
> > >> Dear All,
> > >> I am trying to carry out simulation of protein at 0.5 mM concentration
> > of
> > >> NaCl.
> > >> It has been observed that within few nanosecond ions begin to drift in
> > one
> > >> direction and protein in other direction. I am using Amberff03 force
> > >> filed.
> > >> What may the reason for the same.
> > >>
> > >>
> > > No idea unless you show us your .mdp file and any commands you're
> giving.
> > > Is this drift observed in the raw trajectory, or in something you've
> > > manipulated with trjconv?
> > >
> > > -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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