Re: AMBER: question on simulated annealing

From: David A. Case <>
Date: Tue, 27 Jul 2004 12:26:06 -0700

On Tue, Jul 27, 2004, Venkata S Koppuravuri wrote:

> Following the example in the manual I have heated and cooled the protein
> multiple times starting with the minimized protein (replicates ..... not
> sequentially) using the minimized protein restart file. To my surprise
> the structures in each replicate are identical.

You should not be surprised that running the same calculation over and over
again gives the same result.

> I tried using the IG flag to change the random number seed between
> annealing, but still go the same structure on all annealing runs.

The ig variable is only used to get the starting velocities. But you are
using the default value of tempi of zero, which means that all initial
velocities are zero, no matter what value of ig you use.

You eiher need to generate different starting conformations, or at least
use a non-zero initial temperature, in order to get some randomness into
the calculation.

....good luck...dac

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Received on Tue Jul 27 2004 - 20:53:00 PDT
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