[gmx-users] Re: High frequency output slow down the simulation?

Mark Abraham Mark.Abraham at anu.edu.au
Sat Nov 8 06:13:13 CET 2008

xianghong qi wrote:
> Hello, all:
> I compare the two simulations with different output frequency for .xtc 
> file in same machine. One with low frequency runs  much faster than the 
> one with high frequency. 
> Is that reasonable? I think the frequency shouldn't affect the 
> simulation speed.  
> Anyone has idea about this situation?  Thanks.  

If that's really the only difference between the two simulations, then 
it suggests your file system has severe problems. With modern buffered 
I/O it's inconceivable that writing output could rate-limit GROMACS. 
(Unless something's broken in 4.x, but you haven't said what you're using.)


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