Setting ig=-1 in certain versions of amber (at least 10 and later) will pull
the random seed from the system clock, which is the closest you can get. If
your system clock has coarse precision and you plan to submit all of your
jobs at once using a script, some of your simulations may end up with the
same seed, so you may want to investigate a "pause" or "wait" command in
whatever language you're using.
Good luck!
Jason
On Tue, Sep 7, 2010 at 10:09 AM, Baptiste Legrand <bap.legrand.gmail.com>wrote:
> Thank you Jason and David for your replies. Is it possible to
> automatically generate random ig values and restart a new refinement?
> Thanks
>
> Best
> Baptiste
>
>
> Le 07/09/2010 14:03, case a écrit :
> > On Tue, Sep 07, 2010, Baptiste Legrand wrote:
> >> I'm a new amber user (I'm more familiar with cns). At the moment, I'm
> >> following the tutorial4 on the nmr refinement on a DNA duplex to
> >> determine a modified peptide conformation. All is fine but I'm quite
> >> surprised to have only one structure at the end of the sander run and
> >> not a set of structure. Is there an option to activate or a more
> >> specific protocol to calculate several structures?
> > In Amber, you are expected to run the refinement many times (with random
> > initial velocites, or different starting structures) in order to obtain a
> > family of structures.
> >
> > ....dac
> >
> >
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>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Sep 07 2010 - 09:00:03 PDT
