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 - 09:43:25 CDT

Thanks, Bob. I was asking this because I just submitted a PMEMD job several
days ago with "ig=-1" without knowing this option is not available.

On Thu, Jun 4, 2009 at 10:31 AM, Robert Duke <rduke_at_email.unc.edu> wrote:

> 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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