AMBER Archive (2008)

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

From: Ruchi Sachdeva (ruchi.imt_at_gmail.com)
Date: Wed Aug 13 2008 - 23:09:28 CDT

Dear All,

In one of the previous
lists<http://structbio.vanderbilt.edu/archives/amber-archive/2007/0347.php>in
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
issue?

Thanks in advance

Regards

Ruchi

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu