Read about the image command in cpptraj. There is a lot of discussion in
the archives as well, search for image or autoimage.
On Mon, Aug 27, 2018, 8:34 AM Sanjib Paul <sanjib88paul.gmail.com> wrote:
> Dear Amber Users,
> I am simulating a protein molecule containing
> 259 amino acid residues. I have followed the standard protocol of
> simulation, minimization, heating, equilibration (in NVT and NPT) and then
> production run (NVT) using a rectilinear simulation box and PMEMD.cuda.MPI.
> Starting from the heating step I have been using the 'iwrap = 1' . After
> few nanosecond of production run I have observed that a part of the protein
> molecule has come out of the box. I have attached here an image file for
> the understanding of the condition.
>
> So my concern is if there is any possibility of altering the dynamics or
> any other properties due to this situation. Should I put the protein
> molecule back in the center of box whenever it comes out of the box? Or,
> may I ignore this and continue the production run?
>
> Any fruitful suggestion will be very helpful to me.
>
> Thanking you.
>
> Sanjib Paul
> Research scholar
> Department of Chemistry
> Indian Institute of Technology Kharagpur
> Kharagpur 721302
> India
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Received on Mon Aug 27 2018 - 06:00:12 PDT
