AMBER Archive (2009)

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

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu Mar 19 2009 - 08:24:02 CDT

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 |
>
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