AMBER Archive (2009)

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

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu Jun 04 2009 - 09:31:32 CDT

Well, I would not recommend doing that. It looks to me like there is
nothing to stop one from doing this in the code, but the random number
initialization code clearly states the seed should be > 0. I would have to
dink with it to see what really happens when you do this. The fix to
actually use -1 is pretty simple; I can probably send out a patch at some
point, or some simple directions for folks to hack their own code.

Well, try this:

In mdin_ctrl_dat.fpp, in the subroutine init_mdin_ctrl_dat(),

In the variable declarations, change

integer ifind

to

integer ifind, sec_temp

Right before the "return" in the subroutine init_mdin_ctrl_dat() add the
line:

if (ig .eq. -1) call get_wall_time(sec_temp, ig)

That's it. Really simple, very informal patch.

- Bob

----- Original Message -----
From: "Jifeng Wang" <wangjf_at_gmail.com>
To: "AMBER Mailing List" <amber_at_ambermd.org>
Sent: Thursday, June 04, 2009 10:10 AM
Subject: Re: [AMBER] use of random seed in multiple runs

> 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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