AMBER Archive (2004)

Subject: AMBER: TI with electrostatic decoupling

From: Nelson Fonseca (nfonseca_at_dq.ua.pt)
Date: Tue Nov 23 2004 - 03:56:44 CST

Experience is what you get when you don't get what you
want.

                      -- Dan Stanford--

Dear All,

In order to run a TI free energy calculation with sander,
with electrostatic decoupling, I should run 2 separate
jobs. In the first one, the cahrges are perturbated and in
the last one, the atom type parameters.
My question is if starting, for example from state A to
reach state B, I should pass throug an intermediary state
AŽ, in such a way that from A --> AŽ the charges are
perturbated and from AŽ --> B only the atom type are
changed or if I can reach state B from another way, A
-->B, where the charges are perturbated and starting again
from the same point A --> B, where only the atom types are
perturbated.
Should the inicial geometry from the path AŽ --> B
correspond to the last geometry A --> AŽ where the charges
were changed?

Thanks in advance to all

Regards,

Nelson Fonseca
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