AMBER Archive (2009)

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

From: Robert Duke (rduke_at_email.unc.edu)
Date: Wed Jun 03 2009 - 22:59:48 CDT

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

----- 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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