Re: [AMBER] Query about microsecond long simulation

From: Thomas C. Bishop <bishop.latech.edu>
Date: Wed, 29 Apr 2015 15:03:17 -0500

   I fully agree w/ DAC. there is no scientific reason but some real
   data-management and maybe even policy reasons.
   If the output gets too large (e.g. trajectories > 1 or more reasonably 5 Gb)
   they can be a bit more difficult to transfer/store/manage.
   The specific size is a moving target/matter of taste that depends in what
   resources you have at your disposal
   and how comfortable you are tossing out 1day, 2days or 1 hour of work when
   things go wrong.
   On shared resources these decisions might actually be a matter of policy (no
   jobs longer than 1 day etc...or checkpoints after some many SUs are used)
   or just personal habit/taste.
   Not scientific reasons but real limitations you have to consider anyway.
   TOm

   On 04/29/2015 02:55 PM, David A Case wrote:

On Wed, Apr 29, 2015, Robert Molt wrote:

I apologize for this very elementary question, but I am having
difficulty following parts of this conversation (and I would very much
like to understand all of the wisdom imparted). It was written, below:

"5ns windows is also fine, you might want to extend this to longer if
that is easier for you to manage - I tend to try to shoot for 1 hour or
so run time per simulation -"

I don't know why Ross does it this way, but it's just a matter of taste and
convenience. I generally target about 1 day per individual run: if a machine
crashes, I don't loose more than one day's calculation. But as long as your
script is automatically running job "n+1" as soon as job "n" is completed,
it's up to you how long each job lasts. There is no *scientific* reason to
prefer 1 hr vs 1 day vs 1 week.

....dac


_______________________________________________
AMBER mailing list
[1]AMBER.ambermd.org
[2]http://lists.ambermd.org/mailman/listinfo/amber

References

   1. mailto:AMBER.ambermd.org
   2. http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 29 2015 - 13:30:07 PDT
Custom Search