On Tue, Jun 20, 2017, waleed zalloum wrote:
> I have simulated an enzyme, and I found that it has two different
> conformers. I want to find the free energy path between them and find if
> there is a transition state between these two conformers.
This is one of those questions that is way too general to have any easy
answer. In general, this is a very hard problem, and depends a lot on the
nature of the barrier between the conformers.
Broadly speaking, you need to find some collective ("progress") variable(s)
that describe the change between the conformers. Then the methods described
in Chap. 21 of the Reference Manual may help.
In some cases, you may be able to use the methods described in Chap 20,
without needing to identify collective variables.
....dac
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Received on Wed Jun 21 2017 - 06:30:03 PDT
