AMBER Archive (2009)

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

From: Andrew Voronkov (drugdesign_at_yandex.ru)
Date: Wed Jun 03 2009 - 14:26:48 CDT

Only that I did several runs in this way...ok so I'll remake it.

03.06.09, 17:55, "Gustavo Seabra" <gustavo.seabra_at_gmail.com>:

> 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 <drugdesign_at_yandex.ru> 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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