AMBER Archive (2009)

Subject: Re: [AMBER] use of random seed in multiple runs

From: Gustavo Seabra (
Date: Wed Jun 03 2009 - 08:55:24 CDT

Do you have any reason *not* tuo use a differend random seed for each run?

Gustavo Seabra
Postdoctoral Associate
Quantum Theory Project - University of Florida
Gainesville - Florida - USA
Q: Why do mountain climbers rope themselves together?
A: To prevent the sensible ones from going home.

On Wed, Jun 3, 2009 at 5:28 AM, Andrew Voronkov <> wrote:
> I want to make 30-50 nanosecond run of the protein with explicit waters. But I have limitations on our cluster for time of each job. Can I divide it in several (let's say 5-10 nanosecond runs) without random seed or I need to use random seed in each restart? (output rst -> input rst). Main question of the study is to look at stability of the structure and make average structure from stability parts of trajectpry.
> Best regards,
> Andrew Voronkov
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