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 - 08:30:04 PDT
