it depends on what rdf you want. usually you want to not only center the
solute, but also do a best-fit. how you treat imaging is also important
here. let us know more about your simulation conditions and what you want to
calculate and we can help out.
On Wed, Oct 27, 2010 at 1:15 PM, John S <s.john634.gmail.com> wrote:
> Dear Amber Users
> If I am using nscm =10 in my md protocol , the trajectory so obtained is
> already a centered trajectory .
> Do I need to center it again using ptraj before calculations for radial
> distribution function.
>
> Thanks
> John
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Received on Wed Oct 27 2010 - 11:30:04 PDT
