[gmx-users] Installation of Gromacs and speed...

sharada sharada at ccmb.res.in
Fri Jan 5 08:35:09 CET 2007

Thank you for the reply. I have some more queries:
So if I load Gromacs 3.3.1 on Octane will I gain on the time a bit ? 
Do you suggest me to update the Gromacs versions on both the systems to Gromacs 3.3.1? 
For this do I have to remove the older versions ? Will it over write.
Can I keep both the versions loaded on the system or will there be  a clash ? Do I have to load fftw once again ?
Bothering you with too many questions ! Answers for these would help me to decide .
Thanks in advance.
-- Original Message --
From: "Mark Abraham" <mark.abraham at anu.edu.au>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Thu, 4 Jan 2007 19:32:27 +1100 (EST)
Subject: Re:  Re: [gmx-users] Difference in the Forcefields and speed...
> If I do the MD studies using Gromacs 3.1 and Gromacs 3.3 with differennt
> forcefields like ffg43a1 and ffG53a5 respectively in the same simulating
> conditions how different would be my results ? or will there be any
> difference ?
In theory both forcefield models are accurate representations of reality
over the domain over which they were parametrized. There's no guarantee
that they'd be similar to each other on a given domain, or to reality, and
the further you get from their parameterization domain, the worse the
Ignoring a handful of bug fixes, gromacs 3.1 and 3.3 should produce
similar ensembles, but they cannot be exactly the same.
> Is there a difference  in the speed of the simulations say if I run them
> on SGI Octane R12000 and a Personal computer with 512 RAM Pentium III ?
> Incidently Gromacs 3.1 is loaded on Octane and Gromacs 3.3 on Pentium III
> Why I am asking the second question is that the time taken on Octane is
> much larger ( around 9 days) compared to the Pentium III (3 days) what may
> be the reason ?
Probably, the assembly-language optimized inner loops are being used on
the PIII, and generic inner loops on the Octane. The vast majority of MD
simulation time is spent in these loops, so they are critical to
performance. Obviously, native CPU speed is also an issue here too.
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