AMBER Archive (2008)

Subject: Re: AMBER: Which is best temperature controlling method

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu May 29 2008 - 07:19:22 CDT

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

----- Original Message -----
From: "Germain Vallverdu" <germain.vallverdu_at_lcp.u-psud.fr>
To: <amber_at_scripps.edu>
Sent: Wednesday, May 28, 2008 4:24 PM
Subject: Re: AMBER: Which is best temperature controlling method

>
> David A. Case a wrote :
>
> The best (really only) way to calculate time correlation functions is to
> equilibrate with the thermostat of your choice (usually ntt=3) and then
> run
> NVE simulations. With explicit water, the difference between NVE and NVT
> on
> an equilibrated simualation is quite small.
>
> You are right to be worried about the random part: be sure to select a new
> random number seed for each restart.
>
> ...dac
>
> Dear David
>
> I am sorry but I subscribed recently to the list then I have not the
> beginning of this post.
>
> Can you give more details (or publication) on the fact that in order to
> calculate time correlation functions we have to compute new random
> velocities for each restart ? More precisely, can you say what is the link
> between restarting simulation and calculation of time correlation
> functions ?
>
> Is IG the seed which is used only for computing random velocities ? or is
> it also the same seed that is use to compute random number for langevin
> and andresen temperature controlling algorithm ?
>
> Best wishes
>
> Germain
>
>
> --
> Germain Vallverdu
> Laboratoire de Chimie Physique
> Université Paris Sud 11
> germain.vallverdu_at_lcp.u-psud.fr
> 01 69 15 30 38 / 06 88 59 08 87
> /Chacun de nous a son étoile. Suivons la en nous félicitant de la voir
> chaque jour un peu plus loin !/ (V. Grignard)
>
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