AMBER Archive (2009)

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

From: Robert Duke (rduke_at_email.unc.edu)
Date: Wed Feb 18 2009 - 08:15:00 CST


Given that I had the option to rerun the system relatively easily, and care
about the details of the results, I would do at least the first half again
with proper randomization of ig to see if I saw any significant difference
(compared to the other first half). Carlos is absolutely right that this
problem is not always a killer. It depends on a number of factors including
the nature/size of the system and the frequency of restarts (this off the
top of my head without actually going back to look at the paper myself). I
do know that under some conditions the artifacts can be really really bad.
I think we have tried to warn folks about this, but we really have to modify
the amber code to make reuse of ig in a situation like this harder to
ignore); we intend to do this for amber 11).
Regards - Bob

----- Original Message -----
From: "Carlos Simmerling" <carlos.simmerling_at_gmail.com>
To: "AMBER Mailing List" <amber_at_ambermd.org>
Sent: Wednesday, February 18, 2009 9:04 AM
Subject: Re: [AMBER] IG not change at each restart of NPT simulation

I'm not sure sure that I would be that worried- people have done this
for a while and gotten pretty reasonable agreement with expts. I think
in theory there is a problem, but it's not really that clear that it
causes severe problems in large, complex systems. I'm not saying that
I disagree with Bob, or the paper cited, just that one needs to be
careful in looking at the past and saying that since we found a
potential problem that we should throw out our old work. Clearly much
good work was done with older force fields that we not optimal, and so
on. We make lots of approximations in our work, and we often improve
them but if you understand the limitations of certain methods it
doesn't mean work done with them should be discounted. It's not as
simple as saying that simulations with highly complex systems that
used the same ig value and Langevin thermostat are not acceptable.
nothing we do is perfect- the challenge in being successful in this
field is in understanding and managing the limitations.

On Wed, Feb 18, 2009 at 8:57 AM, Robert Duke <rduke_at_email.unc.edu> wrote:
> Jeffrey,
> Sorry, but I would be worried if I were you. Please see the following
> paper:
> Cerutti, Duke, et al., "A Vulnerability in Popular Molecular Dynamics
> Packages Concerning Langevin and Anderson Dynamics", J Chem Theory and
> Computation 4, 1669 (2008).
> Best Regards - Bob Duke
>
> ----- Original Message ----- From: "Jeffrey" <jeffry20072008_at_yahoo.cn>
> To: "AMBER Mailing List" <amber_at_ambermd.org>
> Sent: Wednesday, February 18, 2009 7:49 AM
> Subject: [AMBER] IG not change at each restart of NPT simulation
>
>
>> Dear all,
>>
>> I read previous posts discussing ntt=3 or 1 for NPT simulation. I
>> performed a 30-ns npt trajectory using ntt=3 and ig=default at each
>> restart
>> (1.6 ns per segment) to monitor the conformational dynamics of a protein
>> system. But some posts have mentioned that IG should change its value at
>> each restart otherwise artiactual behavior can be observed. I'd like to
>> know
>> more in detail about how ig=default at each restart will effect my
>> observation when I only concern on the conformational dynamics? Should I
>> rerun the simulation from just the starting model?
>>
>> Many thanks.
>>
>>
>> ----
>> Jeffrey
>>
>>
>> I pasted here one of the relating posts by Bob.
>> ---------
>> Germain -
>> ig is used for computing random velocities during a restart that does NOT
>> have velocity information (eg., from a minimization), and for the
>> andersen
>> and langevin thermostats (ntt 2, 3 respectively). You can get
>> artifactual
>> behaviour in the thermostats if you use the same seed in restarts, as you
>> need to be effectively sampling from a gaussian distribution over the
>> entire
>> run, not resampling from the same sequence of pseudorandom numbers
>> repeatedly. So in using these thermostats it is important to be careful
>> about changing the value of ig through your restarts, or strange things
>> can
>> happen. There is a facility in sander to use the system clock to get the
>> random seed, probably only in amber 10 (sorry, I don't have amber 10 doc
>> available at the moment), and don't see it described in 9). I don't have
>> this capability in pmemd yet. The best way to do this stuff is to carry
>> the
>> state of the rng forward between restarts; I plan to do that in pmemd in
>> the
>> future.
>> Regards - Bob Duke
>>
>>
>> __________________________________________________
>> ϿעŻ?
>> http://cn.mail.yahoo.com
>>
>>
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