Re: [AMBER] Number of Cycles

From: Robert Duke <>
Date: Tue, 15 Dec 2009 08:16:51 -0500

I presume that for sander there is indeed a simple "default" ntwr value,
giving a rewrite every 500 steps. In pmemd, the value is actually scaled as
a function of processor count once you have more than 10 processors, in
order to not increase the frequency in time of rewriting restart files as
you run on more and more processors. This keeps you from getting into a
situation where writing this file has a significant performance impact.
Regards - Bob Duke
----- Original Message -----
From: "Jason Swails" <>
To: "AMBER Mailing List" <>
Sent: Tuesday, December 15, 2009 7:10 AM
Subject: Re: [AMBER] Number of Cycles


The exact step that the MD died on is fairly irrelevant. The only
thing that really matters is the last step of the MD in which a
restart file was written (this is ntwr, which has a default of 500 I
believe). If ntpr is greater than ntwr (especially by multiples of
ntwr), then there is no way of isolating exactly which step your
calculation ended on. This is why I typically use the same values for
ntwr and ntpr (and ntwx for MD simulations). If you do use the same
value for ntwr and ntpr, and the last step printed for ntpr is 66000,
then your restart corresponds to MD step 66000, and you'll need to run
an additional 34000 steps to reach 100000 (66000 + 34000 = 100000).

Hope this helps!

On Tue, Dec 15, 2009 at 3:31 AM, s. Bill <> wrote:
> Dear AMBER
> How can I complete my total number of cycles?
> Say, I had submitted my job for 100000 cycle (nstlim=100000), and due to
> the wall clock time my job stopped at cycle number 66000, I asked to write
> out the output every 5000 cycle (NTPR=5000, NTWX=5000). The problem here
> is how to complete the remaining steps. I am not sure if the remaining
> steps are 44000, it may be in between 44000 and 43500, where my output
> written every 5000.
> So, how can I complete my number of cycles? is there any keyword manage
> this problem?
> Thanks in advance
> S. Bill
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
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Received on Tue Dec 15 2009 - 05:30:02 PST
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