Grace,
it would be fine to continue- after all, if you stop a simulation and
restart it (due to queue limits, etc), it changes the trajectory as much
or more than switching to another computer type (due to the limited
precision
in the restart file).
Carlos
===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
===================================================================
Grace Li wrote:
>Hi Ross,
>
>Thanks again for your explanation. I understand this aspect of differences
>due to rounding differences, but do you think it would be ok to continue
>sampling on my P4 cluster after already running 10 ns on the super
>computer? Would this cause inconsistency in errors in my experiment?
>
>Grace
>
>
>On Fri, 30 Jul 2004, Ross Walker wrote:
>
>
>
>>Dear Grace,
>>
>>
>>
>>>supercomputer. I noticed that after 900 NSTEPs the results starts to
>>>differ as follows:
>>>
>>>
>>Deviations in MD simulations between different architectures is perfectly
>>normal. Especially with parallel runs. What happens is you get rounding
>>differences that propagate over time and give you different (but equally as
>>valid) trajectories. Typically in order to see if things are running
>>correctly we only compare the first 10 or 20 steps of a simulation. The SGI
>>architecture is also very different to a P4's architecture, one is 64 bit
>>the other 32 bit for example, and so the rounding differences between the
>>two machines will be more acute than if they were based on more similar
>>hardware.
>>
>>Note, though, if you run the same simulation a 100 times on the SAME machine
>>you should see identical trajectories. If you don't then something is very
>>wrong.
>>
>>All the best
>>Ross
>>
>>/\
>>\/
>>|\oss Walker
>>
>>| Department of Molecular Biology TPC15 |
>>| The Scripps Research Institute |
>>| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
>>| http://www.rosswalker.co.uk/ | PGP Key available on request |
>>
>>
>>
>>
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Received on Fri Jul 30 2004 - 20:53:00 PDT
