On Mon, Jul 26, 2010, istvan.kolossvary.hu wrote:
> I attached my .cfg file for reference. I have not changed
> any of the parameters, but turned off most of the I/O and the
> so-called Glue option (to keep members of a complex together in the
> trajectory file that got "separated" by PBC) since the water molecules
> are free to diffuse wherever they want. Depending on your file system,
> etc., Desmond performance can be severely affected by I/O and thus
> biasing benchmark results.
A follow-up question about I/O: the Amber benchmark saves coordinates into
a "trajectory" file every 2ps (i.e. every 1000 steps), and also prints out
energy information at the same frequency. It's not clear that your proposed
cfg file produces similar information (e.g. it has no "trajectory" block).
Could you show how to dump energies and coords every 1000 steps?
Of course, both pmemd and desmond probably run faster if you really limit
I/O, but saving info every 2ps used to be considered "typical", and so is
a part of this benchmark. As people run longer trajectories, they may want
to save fewer intermediate results, but that is a discussion for another day.
...thanks!....dave
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Received on Sun Jul 25 2010 - 20:30:03 PDT
