Re: AMBER: system size limit

From: David A. Case <>
Date: Sun, 23 Jan 2005 22:56:30 -0800

On Mon, Jan 24, 2005, Guanglei Cui wrote:
> I have a question about the upper limit of system size that sander8 can
> handle. Is it possible to model the size of a few hundred thousands of
> atoms?

Look at (and try!) the system in amber8/benchmarks/rt: this has 141,000
atoms. I have run at some point a system about twice as big as these....
The generaly problem with systems much bigger than this is that you can't
afford to do anything interesting with them, because they are too slow.
But Amber is supposed to work with systems of the size you describe.

> I tried the system on two different hardware setups. On Lemieux,
> it says "error: EXCLUDED_ATOMS_LIST not found in parm file". On a local
> cluster, it goes slightly further, but generates no more output after
> reading group definition in a few hours (ntpr = 50) ... Your input is
> highly appreciated.

Offhand, these don't really sound like errors related to the size of the
system. Of course, you should set ntpr=1 when beginning a new system, esp.
if it seems to be giving problems.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Mon Jan 24 2005 - 07:53:00 PST
Custom Search