AMBER Archive (2008)

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

From: Germain Vallverdu (
Date: Wed May 28 2008 - 15:24:55 CDT

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.


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 Vallverdu
Laboratoire de Chimie Physique
Université Paris Sud 11
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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