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
>>>>>>> >
>>>>>>> > _______________________________________________
>>>>>>> > AMBER mailing list
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Received on Fri Jun 05 2009 - 01:12:10 PDT
