AMBER Archive (2006)

Subject: Re: AMBER: Different results between serial and parallel runs in AMBER 8

From: David A. Case (case_at_scripps.edu)
Date: Mon Mar 06 2006 - 20:05:31 CST

On Mon, Mar 06, 2006, Ilyas Yildirim wrote:
>
> I have a question on parallel and serial MD runs in AMBER 8.

It would be better to compare restart runs (irest=1) rather than runs
where random numbers are used to get initial temperature. However,
even the tempi stuff *should* be giving the same results for different numbers
of processors. There may be a funny interaction between ntt=3 and tempi:
it looks like tempi "uses up" some random numbers on the master node,
but these are not equivalently cycled through on the slave nodes. So, then
the random numbers for Langevin will not be the same on the master and slave
nodes....setting irest=1 will avoid this "problem".

Let me know what happens; this buglet appears to still be there in amber9.

...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu