Thanks Jason for reply
I am not asking for any unpublished article I am asking for if there is
any already published (clearly mentioned in my mail) article that will
help to chose me ensemble NVT or NPT for production run.
On 2014-11-03 6:23 pm, Jason Swails wrote:
> 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 Why do you want unpublished articles?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 anonymous unpublished article no more than an anonymous post to an email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
--
----------------------------------------------
Sangita Kachhap
Senior Research Fellow
C/O Dr. Balvinder Singh
Bioinformatics centre
CSIR-Institute of Microbial Technology
Chandigarh, Sector-39A, INDIA
----------------------------------------------
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Received on Mon Nov 03 2014 - 06:30:03 PST
