Hey Carlos,
Ok, that makes sense. Thanks for the suggestion.
Grace
On Fri, 30 Jul 2004, Carlos Simmerling wrote:
> 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 |
> >>
> >>
> >>
> >>
> >>-----------------------------------------------------------------------
> >>The AMBER Mail Reflector
> >>To post, send mail to amber.scripps.edu
> >>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >>
> >>
> >>
> >-----------------------------------------------------------------------
> >The AMBER Mail Reflector
> >To post, send mail to amber.scripps.edu
> >To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
> >
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Jul 30 2004 - 21:53:01 PDT
