[gmx-users] Same starting structure but different trajectories

Emanuel Peter Emanuel.Peter at chemie.uni-regensburg.de
Wed Feb 17 10:17:43 CET 2010

Dear Erik,

I still have some trouble to understand. 
Could you give me a more detailed answer why I get two different 
trajectories on the same machine? It should have the same registers and 
numerical chaos should be exactly the same in that case.



>>> Erik Marklund  02/17/10 10:05 AM >>>
Well, unfortunately it doesn't. Numerical differences are introduced 
here and there for different resasons. On some machines the registers 
have more bits than you'd normally fit into a float or double, and hence 
give higher precision. If those registers are pushed to the stack, then 
the trailing bits get lost. This can happen due to thread scheduling or 
hardware interrupts. Such small differences between runs will over time 
build up to arbitrarily large differences because of the (numerically) 
chaotic nature of MD simulations. When a program is parallelized even 
more sources of such differences arise, since it's e.g. not known 
beforehand in which order certain floats/doubles are added together, 
which in turn may have a small effect on the results.


Emanuel Peter skrev:
> Hi Tsjerk,
> I ran my job on the same machine and made exactly the same inputstructure and 
> inputfile. 
> What does chaos mean in your opinion? A computer should do exactly the same 
> every time you start with the same starting conditions on the same machine.  
> I have to couple my ligand seperately and not as part of my protein, so I can't 
> couple just two groups named Protein and Non-Protein.  
> Bests,
> Emanuel 
>>>> Tsjerk Wassenaar  02/17/10 9:40 AM >>>
> Hi Emanuel,
> Anything small can cause trajectories to diverge, it's chaos. The
> machine on which is run can make the difference. This is also covered
> in the list archives.
>> ;Temperature coupling
>> tcoupl           = nose-hoover
>> tc-grps          = protein NA+ CFP SOL
>> tau_t             = 0.1  0.1 0.1   0.1
>> ref_t             = 300 300 300 300
> This is bad practice. Where did you get that from? Not from any _good_
> tutorial, surely. Check
> http://www.gromacs.org/Documentation/Terminology/Thermostats to learn
> more.
> Cheers,
> Tsjerk

Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys

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