Re: AMBER: Which is best temperature controlling method

From: David A. Case <case.scripps.edu>
Date: Thu, 29 May 2008 07:35:36 -0700

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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Received on Sun Jun 01 2008 - 06:07:33 PDT
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