AMBER Archive (2008)

Subject: AMBER: how to choose the appropriate ensemble for a given problem

From: Ruchi Sachdeva (
Date: Wed Aug 13 2008 - 23:09:28 CDT

Dear All,

In one of the previous
response to GPCR-membrane simulation, Ross Walker has suggested to do
initial heating to say 100 K in NVT ensemble and then switch to NPT for
further heating as calculation of pressure is inaccurate at low
temperatures. I have a query in this context - Is it particularly for
proteins simulated in membrane or a protein simulated in any other
environment such as water? Can anyone please provide a reference where it
has been reported?

I am setting up a simluation for aqueous environment. I have a general
question regarding the selection of ensembles. The use of nvt or npt
ensemble during a production run depends on which factors? Anyone please
throw some light on this aspect. Is there any paper that discusses this

Thanks in advance



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