Re: [AMBER] Query about microsecond long simulation

From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Thu, 30 Apr 2015 07:51:00 -0300

> Em 29/04/2015, à(s) 16:55, David A Case <case.biomaps.rutgers.edu> escreveu:
>
> 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.
>

Risking being wrong (only Ross can give the exact reason here), I’d guess it may be an (overzealous?) attempt to avoid the Langevin synchronization effect, described above by Jason, since you get a chance to change the random seed about every hour.

Cheers,
Gustavo.

Gustavo Seabra




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Received on Thu Apr 30 2015 - 04:00:04 PDT
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