AMBER Archive (2009)

Subject: Re: [AMBER] IG not change at each restart of NPT simulation

From: Rajesh Raju (Rajesh.Raju_at_postgrad.manchester.ac.uk)
Date: Fri Mar 20 2009 - 08:20:09 CDT

Hi,
Thanks. So I just need to put ig= (any number ) in each restart run.
Would it make any difference in my simulation ? Should i change ig
value for each restart evenif there is constraints ?
Thanking you in advance
Rajesh

Quoting "Robert Duke" <rduke_at_email.unc.edu>:

> Yes, I understand that the thing has deeper "state" than just the last
> number (have looked at the code, there are 100 numbers of "state"). So
> I understand in theory what you are saying, and don't disagree - very
> very high liklihood that the next number you choose is okay, as long as
> it is a different number (probably would take work to pick a bad one).
> But there is no harm in doing things that are even more likely, though
> not certain, to not produce problems, so I tend to err in that
> direction; in reality we should really be preserving the state of the
> rng across runs to just be sure. People did not believe that problems
> could occur by reuse of the same random seed; they were wrong. I
> actually hesitated to reply to this thing because I figured someone
> would jump on me about this; sorry, but time and again I see people
> being cocky in this field about cavalier approaches being okay.
> Regards - Bob
>
> ----- Original Message ----- From: "Adrian Roitberg" <roitberg_at_qtp.ufl.edu>
> To: "AMBER Mailing List" <amber_at_ambermd.org>
> Sent: Thursday, March 19, 2009 9:30 AM
> Subject: Re: [AMBER] IG not change at each restart of NPT simulation
>
>
>> Bob,
>> NONONO.
>> Any number is as good as any other number !
>>
>> The random number generators we use are chaotic vs random seed.
>> What this means is that if you change the value of ig by ONE, you
>> get a completely different random sequence.
>>
>> Adrian
>>
>> Robert Duke wrote:
>>> Well, what you want to do is select numbers less likely to repeat
>>> the previous last random number sequence. I have not thought
>>> about this deeply, but based on something I read somewhere, I
>>> believe that choosing prime numbers as seeds has merit. There are
>>> great lists of primes at the website primes.utm.edu (thanks to
>>> Chris Caldwell); that's what I use. Ultimately we (the amber dev
>>> guys, me in particular) should implement code that allows
>>> continued sampling from the distribution first used in a run (so,
>>> basically, saving the state of the pseudo-random number generator
>>> at the end of each "leg" of a run). This unfortunately will
>>> entail dinking with the restart file format.
>>> Regards - Bob Duke
>>> ----- Original Message ----- From: "Rajesh Raju"
>>> <Rajesh.Raju_at_postgrad.manchester.ac.uk>
>>> To: <amber_at_ambermd.org>
>>> Sent: Thursday, March 19, 2009 8:54 AM
>>> Subject: RE: [AMBER] IG not change at each restart of NPT simulation
>>>
>>>
>>> Hi,
>>> I have a doubt... I am using NTT=3 thermostat for my dynamics. after
>>> my equilbration I have done production run atNVT ensemble. Should I
>>> need to change IG random generator seed for restart. I am doing 2ns
>>> with 3-4 restatrs. But dont know how to change ig ...Can i select any
>>> number?
>>> Cheers
>>> Rajesh
>>>
>>>
>>> Quoting "Hopkins, Robert" <hopkins_at_uhcl.edu>:
>>>
>>>> Hi Ross,
>>>>
>>>> Thanks for your prompt and clear reply -- Yes, I'm using NTT = 3, so
>>>> I'll be setting IG for each restart!
>>>>
>>>> Bob Hopkins
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
>>>> Behalf Of Ross Walker
>>>> Sent: Wednesday, March 18, 2009 6:07 PM
>>>> To: 'AMBER Mailing List'
>>>> Subject: RE: [AMBER] IG not change at each restart of NPT simulation
>>>>
>>>> Hi Bob,
>>>>
>>>>> After trying to follow this thread and reading the Cerutti, Duke, et.
>>>>> al. paper, my lack of experience with Amber still leaves me with some
>>>>> questions about my restart runs. Here's the problem: if I restart
>>>>> after a minimization (or if NTX .lt. 3 .and. TEMPI .ne. 0.0), it is
>>>>> clear that the pseudo-random number generator (PRNG)comes into play
>>>> and
>>>>> I would want to use a new IG each time. On the other hand, I assume it
>>>>> is *not* involved with restarting a sander run from a .rst file which
>>>>> contains the velocity information. So, if this is not the case, then
>>>>> I'd really like to know that.
>>>>>
>>>>> What is bothering me is that I'm (no doubt, naively) having difficulty
>>>>> imagining the situation when one would do a long series of linked
>>>>> calculations while resetting the initial velocities at each restart.
>>>> In
>>>>> this case, the consequences of not specifically changing the IG value
>>>> at
>>>>> each restart in order to find an initial, 'non-repetitive' set of
>>>>> velocities seem apparent. Alternatively, (and the crux of my concern)
>>>> it
>>>>> may be that the PRNG is used elsewhere (embedded in the Amber code)
>>>> and
>>>>> the reason for changing the IG value is not explicitly apparent.
>>>>
>>>> What you are describing is correct if you do not use a thermostat or you
>>>> use
>>>> a Berendsen thermostat. In this case the random number generator is not
>>>> used
>>>> unless you are randomly assigning velocities which you do not do on a
>>>> restart. However, the paper and the discussion is refering to the case
>>>> where
>>>> the Langevin thermostat is used (ntt=3) here the random number generator
>>>> is
>>>> used to drive the Langevin thermostat and it is this situation that
>>>> causes
>>>> the problems. Since if you keep reusing the same random number stream
>>>> you
>>>> essentially impart a series of correlated forces on your system which
>>>> can
>>>> cause all sorts of weird things to happen. Thus if you have ntt=3 you
>>>> MUST
>>>> change the value of IG for every run including restarts. With AMBER 10
>>>> and
>>>> later you can set this to -1 and it will use the wallclock time in
>>>> microseconds and save you needing to script the change yourself.
>>>>
>>>> I hope this answers your concerns.
>>>>
>>>> All the best
>>>> Ross
>>>>
>>>>
>>>> /\
>>>> \/
>>>> |\oss Walker
>>>>
>>>> | Assistant Research Professor |
>>>> | San Diego Supercomputer Center |
>>>> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
>>>> | http://www.rosswalker.co.uk | PGP Key available on request |
>>>>
>>>> Note: Electronic Mail is not secure, has no guarantee of delivery, may
>>>> not
>>>> be read every day, and should not be used for urgent or sensitive
>>>> issues.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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>>
>> --
>> Dr. Adrian E. Roitberg
>> Associate Professor
>> Quantum Theory Project
>> Department of Chemistry
>>
>> Senior Editor. Journal of Physical Chemistry
>> American Chemical Society
>>
>> University of Florida PHONE 352 392-6972
>> P.O. Box 118435 FAX 352 392-8722
>> Gainesville, FL 32611-8435 Email adrian_at_qtp.ufl.edu
>>
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