Re: [AMBER] Query about microsecond long simulation

From: David A Case <case.biomaps.rutgers.edu>
Date: Wed, 29 Apr 2015 15:55:18 -0400

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


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Received on Wed Apr 29 2015 - 13:00:07 PDT
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