On Mon, 2014-11-03 at 10:37 +0530, Sangita Kachhap wrote:
>
> Hello AMBER users
>
> Is there any published article regarding selection of NVT/NPT ensemble
> for production run?
Why do you want unpublished articles? If they are about to be
published, people are unlikely to share them. If they are not about to
be published, there may be a good reason for that. I would trust an
anonymous unpublished article no more than an anonymous post to an email
list ;).
Also, there is no *correct* answer. Sometimes you need to use NpT.
Other times there is no difference between NpT and NVT so it doesn't
matter which you use. Still other times you need to use NVE (e.g., for
diffusion or other temporal properties).
When a system is not near a phase transition, the NVT and NpT ensembles
are equivalent, since water is nearly incompressible. Since NVT
simulations are more efficient (how *much* more efficient depends on the
barostat algorithm and code base you are using), people often use NVT
for production calculations when given the choice since they can sample
more in the same amount of time.
When the system _is_ near a phase transition (e.g., a large
conformational change is expected in a protein, etc.), the two ensembles
can differ a lot and the choice becomes important.
If you want help determining which one to choose you have a couple
routes:
1. Read *published* papers performing similar calculations to the ones
you are attempting and see what they use.
2. Try both -- see if your answers differ. If the difference is
statistically relevant, pick the one that best models the reality you
are trying to simulate.
3. Err on the side of caution and just use the ensemble that corresponds
to the experimental conditions you are trying to model -- this is
usually NpT.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Nov 03 2014 - 05:00:03 PST
