AMBER Archive (2009)

Subject: Re: [AMBER] Number of Cycles

From: Jason Swails (jason.swails_at_gmail.com)
Date: Tue Dec 15 2009 - 07:34:29 CST

Last detail I forgot, promise:

On Tue, Dec 15, 2009 at 8:32 AM, Jason Swails <jason.swails_at_gmail.com> wrote:
> 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

The number is the time, in picoseconds, rather than the timestep per
se. The time is, however, listed in picoseconds in the mdout file.

> 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...
>
> Good luck!
> Jason
>
>
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032

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