Use Langevin dynamics (the sd integrator) to control the temperature.
You are sure to get the correct ensemble that way and if you are doing
US then you can not extract dynamics anyway.
Hopefully somebody else can address the pressure coupling for you, but
probably you need to provide more information to get a useful answer
there.
-- original message --
Dear all,
I want to use umbrella sampling to calculate the PMF of the
conformational transition of a protein. What temperature coupling method and
pressure coupling method should I use? Berendsen temperature coupling or
Nose-Hoover temperature coupling? Or each one is OK?
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