RE: [AMBER] Number of Cycles

From: Niel Henriksen <>
Date: Tue, 15 Dec 2009 11:11:08 -0700

>If nstlim is evenly divisible by ntwx, then the last mdcrd trajectory frame
>written should I believe correspond to the final restart file. The
>important thing to remember, is that the restart file will always be written
>at the final step of the run, regardless of the value of ntwr.

Yes I agree. If all my jobs ended before the wallclock limit there would be no
problem. However, I am greedy with every second I get, so all of my jobs get
killed before they end "normally". Thus, to ensure that I don't have redundant
data, I like to write restart files with every trajectory frame. (I also write 2 restart
files each ntwr so that if one gets only partially written I have a back-up). I suppose
I should evaluate whether this approach maximizes the use of resources and
minimizes the total (real) time to complete a simulation.

Off the top your head, if I use somewhere between 32 - 64 processors on a
teragrid machine (say ranger or kraken) for a simulation with 40,000 atoms,
would I get a big performance impact with ntpr=ntwx=ntwr=500?

AMBER mailing list
Received on Tue Dec 15 2009 - 10:30:01 PST
Custom Search