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 Fri Jun 05 2009 - 01:12:15 PDT
