Thank you
On Fri, Apr 25, 2014 at 11:11 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Fri, 2014-04-25 at 10:32 -0400, Lara rajam wrote:
> > Dear Amber
> >
> > I am doing a MD simulation in amber
> >
> > I followed all the steps as per the tutorials
> >
> > In production run I found the molecule is coming out of the box sometime
> > and goes back
> >
> > is it a problem how to fix this or since it is in PBC nothing to worry ,
> I
> > am not clear
>
> This is an imaging artifact arising from the use of PBC. You can use
> the "autoimage" command in cpptraj to make everything look "pretty"
> again, but this is just for your benefit when visualizing. It has no
> effect on results.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Fri Apr 25 2014 - 08:30:05 PDT
