I agree with John Cannon that the general standard idea is to just use
ig=-1, but still, what you did should have produced different results.
I've never used ntt=1, but I have a series of runs going using ig=-1 and
ntt=3 that all started from the same equilibration endpoint. I'll post
another reply once I've looked at them to let you know if they are actually
different.
Also, to what extend are the runs identical? Do they have 0 RMSD across
all frames?
~Aron
On Fri, Feb 24, 2012 at 11:43 AM, Cannon, John F. <
CannonJ.health.missouri.edu> wrote:
> My understanding is that you use ig=-1 if you want a different random seed
> for velocities.
>
> John Cannon
> Genetics Program Chair and
> Associate Professor of
> Molecular Microbiology and Immunology
> University of Missouri
> 1 Hospital Drive
> Columbia, Missouri 65212
>
>
> -----Original Message-----
> From: Oliver Kuhn [mailto:oak.amber.googlemail.com]
> Sent: Friday, February 24, 2012 10:37 AM
> To: AMBER Mailing List
> Subject: [AMBER] same simulation using different random seeds on GPU
>
> Hi.
>
> I want to use differing initial random velocities for simulations running
> on GPU.
> That has always been working on CPU, but on the GPU I get exactly the same
> simulation.
>
> For example, input 1 is:
>
> production simulation (NPT) - 2 ns
> &cntrl
> ig=1,
> irest=0,ntx=1,
> nstlim=1000000,dt=0.002,
> temp0=300.0,ntt=1,tautp=1.0,
> ntc=2,ntf=2,
> cut=9,
> ntpr=500,ntwx=500,ntwv=0,ntwe=500,iwrap=1,
> ntb=2,ntp=1,pres0=1.0,taup=1.0,
> ntr=0
> /
>
> and another input has ig=41
> giving me same simulations!?
>
> As I googled, I found a comment from Ross that GPU uses different random
> number generators.
> I'm quite sure he does not mean also different syntax in using it.
> Has anyone experienced similar problem and can help me?
>
> Greets,
> Oliver
>
> --
> Oliver Kuhn, Department of Bioinformatics, Center for Medical
> Biotechnology, University of Duisburg-Essen, Universitätsstr. 1-5, 45141
> Essen, Germany phone +49 201 183-3121, oliver.kuhn.uni-due.de_______________________________________________
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>
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--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Fri Feb 24 2012 - 09:00:03 PST
