AMBER Archive (2008)

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

From: David A. Case (case_at_scripps.edu)
Date: Thu May 29 2008 - 09:35:36 CDT

On Wed, May 28, 2008, Germain Vallverdu wrote:
>
>
> 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 ?

As Bob kind of said, the random number seen only affects initial velocities
(when irest=0) or when you are using a thermostat like ntt=2 or 3.

To compute time correlation functions, you want NVE simulation (with ntt=0);
you also want to begin from a well-equilibrated system (hence will be using
irest=1). Thus, the random seed would have no effect on such simulations.

...dac

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