[gmx-users] Ions drifting

[jani vinod]

Dear Justin and Johnny,
Thank you  for the guidance.


Regards
Vinod

On Thu, Dec 18, 2014 at 7:37 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
>
> If the Na or Cl ion don't strongly bind to the protein, as described by the
> force field, then they might not always bind to and stay with the protein
> in the simulation.
> If that is what you want, I guess you can artificially add a restraint to
> make the ion to stay closer to the protein ... I'm not sure about the
> consequence.
>
> On Thu, Dec 18, 2014 at 5:53 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >
> >
> > On 12/17/14 11:47 PM, jani vinod wrote:
> >
> >> 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.
> >>
> >>
> > This should be simple to do with trjconv -center -pbc mol -ur compact
> >
> > Choose Protein for centering and System for output.
> >
> > -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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