It depends. It can be useful to cluster your trajectories and compare binding energies among different clusters to decide what is an appropriate sampling.
Marcus Arieno
> On Mar 17, 2014, at 6:51 AM, Mary Varughese <maryvj1985.gmail.com> wrote:
>
> Hi,
>
> Does MMPBSA is calculated over the entire trajectory (neglecting
> variations) or 3 to 5 ns of stable region?
>
> Thanking you
>
> --
> Mary Varughese
> Research Scholar
> School of Pure and Applied Physics
> Mahatma Gandhi University
> India
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 17 2014 - 04:30:03 PDT
