AMBER Archive (2009)

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

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Thu Mar 19 2009 - 08:30:10 CDT

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
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>> 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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