AMBER Archive (2009)

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

From: Naser Alijabbari (na3m_at_virginia.edu)
Date: Fri Jun 05 2009 - 10:30:55 CDT

Previously have read a discussion the archives that large prime numbers are
better seeds ( http://archive.ambermd.org/200903/0336.html). Does anyone
have any experience with using large prime numbers, and how large is large
enough (for example ig=103577 vs ig =99999989 which the limit of ig
variable). Don't prng do better using prime numbers?

On Fri, Jun 5, 2009 at 10:45 AM, Robert Duke <rduke_at_email.unc.edu> wrote:

> Hi Gustavo,
> Oh, and if you say, even if the random number distribution generated with a
> -1 seed is statistically good, there remains the problem that with pmemd, if
> you stick in -1 as ig each run, you are correlating the heck out of your
> runs, which we know is very bad. SO folks absolutely should NOT use ig = -1
> with pmemd through amber 10 unless they apply the informal patch I put up on
> the amber reflector yesterday. Everyone should note that random number
> generation in sander and pmemd is intended to be, and is identical, aside
> from this -1 seeding thing that was a new feature added to sander 10 that I
> unfortunately missed when working on pmemd 10. Also note, if you use -1 for
> earlier versions of sander (<10), you are asking for trouble also. We
> should really have implemented this very differently, with a different flag
> for time-based generation of the seed, and should have been checking for
> out-of-range values of ig...
> Regards - Bob
> ----- Original Message ----- From: "Gustavo Seabra" <
> gustavo.seabra_at_gmail.com>
> To: "AMBER Mailing List" <amber_at_ambermd.org>
> Sent: Friday, June 05, 2009 9:28 AM
> Subject: Re: [AMBER] use of random seed in multiple runs
>
>
> 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.
>> [...]
>>
>
> Bob, please correct me if I'm wrong here but, looking at the
> random.fpp file in pmemd/src dir, it lloks like the seed provided by
> the amber input is used to generate two internal seeds, is1 and is2:
>
> =======================================================
> data is1max, is2max /31328, 30081/
>
> ! Construct two internal seeds from single unbound Amber seed:
> !
> ! is1 and is2 are quotient and remainder of iseed/IS2MAX. We add
> ! one to keep zero and one results from both mapping to one.
> ! max and min functions keep is1 and is2 in required bounds.
>
> is1 = max((iseed / is2max) + 1, 1)
> is1 = min(is1, is1max)
>
> is2 = max(1, mod(iseed, is2max) + 1)
> is2 = min(is2, is2max)
> ========================================================
>
> So, if you enter a seed of "-1", both is1 and is2 will end up being 1.
> There's nothing "illegal" about that, but then you are again always
> running your calculation with the same seeds.
>
> Gustavo.
>
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