Hi,
this is not a discussion connected to Amber, but something general about
molecular simulations. I would say the honest answer is clearly "No" in
most cases. What you get should be a structure of low energy compared to
exactly that part of phase space your simulation explored. The structure
you get will therefore be very dependent on your starting coordinates. You
need additional justification if you want to use it as a model for the
global minimum.
This problem, often called the "sampling problem" is explored in many good
textbooks on MD in some detail and it is at the core of understanding what
simulation can and cant do.
Kind Regards,
Thomas
On Sun, July 15, 2012 5:56 am, jit mukherjee wrote:
> Dear Amber Users,
> I am new to Amber. Can the structure obtained after simmulation be taken
> as
> the reasonable global minimum? Please give your view.
>
> Regards,
> jit
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Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Sun Jul 15 2012 - 06:00:05 PDT
