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 - 07:57:35 CST

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
>
>
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