On Tue, Feb 13, 2007, Ichinkhorloo Erdenebaatar wrote:
> Jagshemash! [means 'Hello Everybody!' in Mongolian]
>
> I hope that everybody in the high-performance computing have
> already heard about the "dynamic memory of AMBER" -- revolutionary
> new concept routinely employed in recent releases of AMBER.
[Note that if your interest is in performance, you should use pmemd, if
possible.]
>
> + ix(1:lasti) = 0 ! hurts performance, .#$!.$#
> +
> Without this
> line 'ix(1:lasti) = 0' the SANDER
> of AMBER does malfunctioning sometimes. In particular, a part of the
> array determines whether apply SHAKE to some bond or not.
Thanks for the report. Do you know what part of the ix() array is the
culprit? I looked through the obvious places where shake() uses the
ix() array, and all those places appeared to be initialized. I ran the
test cases with and without the above patch, and did not see
differences. Do you a particular example that illustrates the problem?
[Also, what compiler/OS are you using?]
...thanks...dac
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Received on Sun Feb 18 2007 - 06:07:08 PST
