[gmx-users] Difference in the Forcefields and speed...

[Mark Abraham]

> 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
chances.

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

Yep.

> 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.

Mark