From: Dr. Eddie (eackad_at_gmail.com)
Date: Mon Aug 31 2015 - 14:02:46 CDT
Hello all,
I have a simple question which I know does not have a simple answer: what
is the largest sampling frequency (dcd output) I need?
I'm looking for any theoretical work on how to know when: 1) the system has
converged 2) the sampling rate of the system is sufficiently small to NOT
alias too much information?
I understand in work with conformational changes in the protein this is not
an issue. However, for those working on studying the steady-state
behaviour, how do you tell when your system has a "good" sampling of the
conformational space so you can extract statistically relevant information
from it? My goal is to understand this for regular MD so that In can use
replica exchange which (hopefully) will give the same information in less
time.
Any references or help would be very helpful!
Thanks,
Eddie
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