AMBER Archive (2009)
Subject: Re: [AMBER] Number of Cycles
From: Jason Swails (jason.swails_at_gmail.com)
Date: Tue Dec 15 2009 - 07:32:31 CST
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.
Correction to my previous email, but I forgot about a feature of the
restart file. The restart file begins with a title line (may be
blank). The very next line has two numbers. The first number is the
number of atoms in the system. The second number is the time step of
the restart file. Thus, you should be able to correlate this back to
which step it died on. The mdout file should tell you the time of the
first step, and knowing your timestep (dt), you should be able to
calculate how many steps were taken before the final restart was
written. Everything else in my email (except asserting that there is
no way of knowing exactly what step the simulation died on) is true...
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
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