AMBER Archive (2009)

Subject: Re: [AMBER] Number of Cycles

From: Jason Swails (jason.swails_at_gmail.com)
Date: Tue Dec 15 2009 - 06:10:02 CST

Hello,

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!
Jason

On Tue, Dec 15, 2009 at 3:31 AM, s. Bill <s_bill36_at_yahoo.co.uk> 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
>
>
>
>
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-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032

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