[gmx-users] Using GROMACS to do colloid simulations

[Yang Ye]

Perhaps you shall look Espresso (http://www.espresso.mpg.de/) for 
coarse-grain simulation. Espresso saved my PhD thesis after spending 
more than one year's time in engaging GROMACS to do what I desired.

Because of the size of the colloid simulation system, the expensive PME 
calculation will drag GROMACS' fastest non-bonded calculation to make it 
not so fast. GROMACS' mission is to create a specialized and highly 
optimized engine. Espresso allows you to prototype the simulation system 
and provides more freedom without going to the source code level.

On 9/26/2007 4:13 AM, Rich Hanes wrote:
> Hello,
>
> I recently attended a conference where some of my colleagues were talking about GROMACS and how it was really good and fast. They work with proteins, specifically, the mechanical properties of collections of proteins, eg actin filaments. I am working in Soft Matter Physics, with colloids. I generally work with 1 micrometer PMMA spheres. I can get the interaction potential, charge, radius, polydispersity etc etc to load into gromacs, but I want to know if anyone has used gromacs for colloid simulations, or if I should look elsewhere. Things which might make GROMACS unsuitable are, time and length scales, hydrodynamics. WHat do you think?
>
> Thanks for your help with this,
>
> Richie
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