[gmx-users] Ions drifting

[Tsjerk Wassenaar]

Hi Vinod,

There are no sides in a periodic system. It's merely the visualization. All
the ions on that one side are also on the other.

Cheers,

Tsjerk
On Dec 17, 2014 5:26 AM, "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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