Dear Amber Users:
I've done some SMD simulations with different starting coordinates
taken from equilibrium simulations. I have some questions about
the direction of the force. Can we define the direction of the force in the
SMD simulations? If not, does the method choose the random directions of
the forces? How does it choose the directions during the SMD simulation, by
following the minimum energies in the potential energy surface?
If the directions can not be define, can I assume that the SMD
method in Amber is very similar with the random expulsion molecular
dynamics (RAMD) method?
Hope this helps,
Cuiyl
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Received on Sun May 25 2014 - 19:30:02 PDT
