On Thu, Oct 28, 2010 at 5:11 AM, fancy2012 wrote:
> Dear amber users,
> How could I get the free energy landscape from an amber coordinate?
> Because I want to get the model, which is at the bottom of the energy surface. Thanks very much!
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
What do you mean by that? Do you want to get *the snapshot* with the
lowest potential energy from a trajectory file? If this is the case,
you will need to postprocess the trajectory file (with imin=5) to
obtain energies for each snapshot, then choose the one with lowest
energy.
Good luck,
Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7417
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Received on Thu Oct 28 2010 - 10:00:02 PDT
