[gmx-users] Simulations becoming slower with time

Erik Lindahl lindahl at stanford.edu
Wed Dec 11 20:31:34 CET 2002

David wrote:

>I'm running a series of simulations on 4 processors. It's a big system
>(19200 atoms) with PME. Since the queueing system limits me to 1 day
>jobs, I cut the simulation in pieces of 250 ps. The first six
>simulations finish within a day, the seventh however doesn't anymore
>(reproducibly). See below for timings. The amount of operations
>(according to the log files) does not increase, files are equally
>long... Density is constant too. Has anyone noticed something similar? 
>Simulation	Run time (s)
>0  		61873.000 
>1  		70679.000 
>2  		76894.000 
>3  		77988.000 
>4  		79592.000 
>5  		83272.000 
>6  		84194.000 
Hi David,

Could it be water sorting?



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