OK, thanks for a nice tip !
Best,
Marek
Dne Fri, 05 Jun 2009 21:18:35 +0200 Gustavo Seabra
<gustavo.seabra.gmail.com> napsal/-a:
> You may also want to check this article:
>
> http://pubs.acs.org/doi/abs/10.1021/ct800573m
>
> 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.
>
>
>
>
> 2009/6/5 Marek Maly <marek.maly.ujep.cz>:
>> Hi Gustavo,
>> thanks for your info and for the simple explanation of the "correlation
>> problem".
>> I just downloaded relevant article:
>>
>> Uberuaga, B.P.; Anghel, M.; Voter, A.F. Synchronization of trajectories
>> in
>> canonical
>> molecular-dynamics simulations: Observation, explanation, and
>> exploitation.
>> J. Chem.
>> Phys., 2004, 120, 6363-6374.
>>
>> but I had no time to read it so far ...
>>
>>
>> Best,
>>
>> Marek
>>
>>
>>
>> Dne Fri, 05 Jun 2009 15:37:42 +0200 Gustavo Seabra
>> <gustavo.seabra.gmail.com> napsal/-a:
>>
>>> 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 - 01:09:39 PDT
