AMBER Archive (2009)

Subject: Re: [AMBER] use of random seed in multiple runs

From: Jifeng Wang (wangjf_at_gmail.com)
Date: Thu Jun 04 2009 - 09:10:50 CDT

On Wed, Jun 3, 2009 at 11:59 PM, Robert Duke <rduke_at_email.unc.edu> wrote:

> Note that the -1 capability is not yet in a released version of pmemd (I
> think we have it in the pmemd 11 codebase).
> - Bob
>

Is it ok to use "-1" itself as a random seed for PMEMD?

>
> ----- Original Message ----- From: "Gustavo Seabra" <
> gustavo.seabra_at_gmail.com>
> To: "AMBER Mailing List" <amber_at_ambermd.org>
> Sent: Wednesday, June 03, 2009 10:00 PM
> Subject: Re: [AMBER] use of random seed in multiple runs
>
>
>
> Any group of simulations using stochastic thermostats, including
> Langevin, is subject to synchronization effects if using the same seed
> for all simulations, and eventually you end up with all correlated
> runs, which influences your statistics. Note that, in Amber10, you can
> avoid that by just using 'ig=-1' in all cases. That will tell sander
> to generate a new random seed every time, I believe based on clock
> time.
>
> Gustavo Seabra
> Postdoctoral Associate
> Quantum Theory Project - University of Florida
> Gainesville - Florida - USA
>
> -------------------------------------------------------------------------------------------
> Q: Why do mountain climbers rope themselves together?
> A: To prevent the sensible ones from going home.
>
>
>
>
> On Wed, Jun 3, 2009 at 3:26 PM, Andrew Voronkov <drugdesign_at_yandex.ru>
> wrote:
>
>> Only that I did several runs in this way...ok so I'll remake it.
>>
>> 03.06.09, 17:55, "Gustavo Seabra" <gustavo.seabra_at_gmail.com>:
>>
>> Do you have any reason *not* tuo use a differend random seed for each
>>> run?
>>> Gustavo Seabra
>>> Postdoctoral Associate
>>> Quantum Theory Project - University of Florida
>>> Gainesville - Florida - USA
>>>
>>> -------------------------------------------------------------------------------------------
>>> Q: Why do mountain climbers rope themselves together?
>>> A: To prevent the sensible ones from going home.
>>> On Wed, Jun 3, 2009 at 5:28 AM, Andrew Voronkov <drugdesign_at_yandex.ru>
>>> wrote:
>>> > I want to make 30-50 nanosecond run of the protein with explicit >
>>> waters. But I have limitations on our cluster for time of each job. Can > I
>>> divide it in several (let's say 5-10 nanosecond runs) without random > seed
>>> or I need to use random seed in each restart? (output rst -> input > rst).
>>> Main question of the study is to look at stability of the > structure and
>>> make average structure from stability parts of > trajectpry.
>>> >
>>> > Best regards,
>>> > Andrew Voronkov
>>> >
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>>
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