[gmx-users] strange jumping in the frames

Mark Abraham mark.abraham at anu.edu.au
Fri Sep 10 11:00:45 CEST 2010

> as you can see the time jumped from 
> 41120.00000       to 41125.00391 , 
> while it has to be 41125.00000 and then it continue the rest of 
> simulation like this,
> Do you what is the problem ?!!

Probably no problem at all. Numbers that are readily represented in decimal notation, like a timestep of 0.002ps, need not have an exact representation in *binary* floating point. If they don't, then when you add up a large number of them, then you can accumulate rounding error. Probably, if you run

grep "0\.00000" *.log

then you will see other times reported that have not rounded nicely.

My best guess is that your simulation stopped at this point, and restarted from the step corresponding to 41125.004ps, and rounding error is doing the rest.


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