Hi Marek,
Notice that this correlation problem does not affect any of your
individual MD runs. Individually, they are all OK, and will give you
the correct results, meaning that this does not introduce any bug or
calculation error, your calculation wil not crash and the results
should be the same irrespective of the random seed.
You will only notice this correlation problem when comparing multiple
simulations of *the same system*. Basically by running multiple
sumulations we expect to get better statistics. However, since they
tend to synchronize if using the same seed, what we would have is just
a bunch of copies of the same simulation, and the statistics are not
as good as we expected.
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.
2009/6/4 Marek Maly <marek.maly.ujep.cz>:
> Hi Carlos,
> thanks for your notice. It is clear to me that the "correlation problem" is
> still present
> in my simulations which I have done using ig=-1 in PMEMD. For this reason I
> pointed out
> the importance to implement this ig value (-1) in PMEMD the same way like in
> SANDER.
>
> For this moment I just hope that this correlation effect is not too big and
> that his influence of
> binding energy of my ligand and receptor will not be so crucial. In this
> moment I am
> just happy that this seed value didn't affect beadly pseudorandom number
> generator and thus also thermostat function.
>
> Best,
>
> Marek
>
>
>
> Dne Thu, 04 Jun 2009 21:20:59 +0200 Carlos Simmerling
> <carlos.simmerling.gmail.com> napsal/-a:
>
>> well keep in mind that changing the see with restarts or between runs is
>> not
>> about the temperature being wrong, it's about correlation of the rng
>> stream.
>> even if -1 works in this pmemd version and gives correct temperature, it
>> doesn't overcome the correlation problem.
>>
>>
>> 2009/6/4 Marek Maly <marek.maly.ujep.cz>
>>
>>> OK, as I noticed before, it seems that you are right and -1 is OK for the
>>> temperature control.
>>> Just for the illustration I attached output file from last 0,5ns of the
>>> 7ns
>>> run which
>>> was performed in T=310K.
>>>
>>> Thanks also for your preliminary "patch" since the reason why ig=-1 was
>>> implemented
>>> in SANDER is in my opinion even more important in PMEMD since probably
>>> the
>>> most researchers
>>> use SANDER just for the "initial" part of the simulation (minim, heat,
>>> density) but for the
>>> production runs use PMEMD since it is faster.
>>>
>>> Best,
>>>
>>> Marek
>>>
>>>
>>>
>>>
>>>
>>> Dne Thu, 04 Jun 2009 19:02:58 +0200 Robert Duke <rduke.email.unc.edu>
>>> napsal/-a:
>>>
>>>
>>> Hi Marek,
>>>>
>>>> It would take a bit of poking, but it could be that the real problem is
>>>> setting the seed to 0, and if you use < 0, then the math in the
>>>> Marsaglia
>>>> rng works out okay; I just have not checked it out and really only
>>>> recently
>>>> noticed that there are no input range controls on ig in pmemd (probably
>>>> because there were none in sander). The reason that sander has the -1
>>>> feature and pmemd doesn't is that no one told me this was being done in
>>>> sander; I can miss new stuff that affects compatibility very easily
>>>> unless
>>>> there is a specific test, because there is a huge volume of other
>>>> irrelevant
>>>> changes as a general rule. Sorry for any trouble caused by this.
>>>> - Bob
>>>> ----- Original Message ----- From: "Marek Maly" <marek.maly.ujep.cz>
>>>> To: "AMBER Mailing List" <amber.ambermd.org>
>>>> Sent: Thursday, June 04, 2009 12:35 PM
>>>> Subject: Re: [AMBER] use of random seed in multiple runs
>>>>
>>>>
>>>> Hi Bob,
>>>>
>>>> I just finished some series of calculations and I have some another in
>>>> progress with setting ig=-1.
>>>> Of course that I really didn't assume that this complementary thermostat
>>>> setting is defined only for SANDER and not for PMEMD so
>>>> I used it also for the production PMEMD runs (using Amber10).
>>>>
>>>> I had no time to do detail analysis yet but after reading of this
>>>> contribution I at least checked the temperature evolution
>>>> and it seems that it is OK (I used Langevin thermostat). I also checked
>>>> visually one of my simulated system and didn't
>>>> see any significant problems.
>>>>
>>>> I have some another simulations with this setting (ig=-1) in progress so
>>>> it is question if it is not worth to
>>>> change ig setting there, but I would like to have all the simulations
>>>> done with the same setting ...
>>>>
>>>> So please when you learn more about possible problems with this setting
>>>> in
>>>> actual version of PMEMD, let me know
>>>> since I need to know if my results are trustable or not. As I already
>>>> mentioned, temperature control seems OK
>>>> but there could be another issues ...
>>>>
>>>> Anyway if some serious "hazards" regarding to this setting in PMEMD will
>>>> be found, would be resonable to
>>>> notice in Amber users manual ( for example in this section: "2.6.8.
>>>> Temperature regulation" ), that
>>>> setting "ig=-1" is not implemented in the actual version of PMEMD and
>>>> that
>>>> it is not recommended
>>>> sice it could cause some serious problems...
>>>>
>>>> Thank you in advance for any additional info to this topic.
>>>>
>>>> Best
>>>>
>>>> Marek
>>>>
>>>>
>>>>
>>>>
>>>> Dne Thu, 04 Jun 2009 16:31:32 +0200 Robert Duke <rduke.email.unc.edu>
>>>> napsal/-a:
>>>>
>>>> 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.gmail.com>
>>>>> To: "AMBER Mailing List" <amber.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.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.gmail.com>
>>>>>>> To: "AMBER Mailing List" <amber.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.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.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.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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Received on Sat Jun 06 2009 - 01:08:00 PDT
