AMBER Archive (2009)

Subject: [AMBER] Equilibration Scaling to System Size

From: Hopkins, Robert (
Date: Tue Feb 24 2009 - 16:31:37 CST

AMBER Users,


I have looked for information about the time required for proper
equilibration vs. system size in a regular MD run, but haven't found
anything very close in the reflector archive.


So, here is my question: from practical experience, *roughly* how does
the system time (not clock time) required for appropriate equilibration
(prior to MD production) scale with total number of atoms (N) in the
system? It seems that a time proportional to somewhere between N^3 and
N! might be on the right track, but surely it also depends on how many
TIP3P waters with limited degrees of freedom are in the system, etc.
So, for example, if a 45,000 atom system needs on the order of 20 ns of
equilibration time, can one estimate how much time a 15,000 atom system
might need?


I would greatly appreciate hearing about anyone's experiences or 'rules
of thumb' relating to this question. Thanks in advance.


Robert Hopkins

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