[gmx-users] Gromacs for Aerosol Particle Agglomeration

[Yang Ye]

On 9/29/2007 9:13 PM, Lorenzo Isella wrote:
> Dear All,
> I am 100% new on this list and to Molecular Dynamics in general.
> This is what I am interested into (and would like to know if Gromacs is
> then the right tool).
> I am not really into biology or chemistry, but rather in aerosol science.
> I am interested in studying how diesel exhaust aerosol particles,
> generally carried by a turbulent exhaust flow, collide and, by
> "sticking" together, give rise to complicated structures (idea of
> agglomeration).
> We now leave aside the technicalities (how they stick, what the
> compenetration depends upon etc.), but first of all I would like to know
> if Gromacs is the right tool for doing that.
You may consult the gromacs manual, which is also a good introductory 
material on the topic of MD. You need to check especially whether the 
interaction existed in your system can be found in GROMACS' supported 
inter-particle interaction.
> Typically, I deal with concentrations around 10^8 particles per cm^3 and
> I need to follow the evolution of the system for some seconds.
> The particles carrier-flow is typically turbulent, but collisions are
> mainly due to Brownian motion (I am thinking about some Langevin 
> dynamics).
> I have access to a few nodes in a cluster (if that becomes a necessity)
> but have no experience in running parallel codes.
You can leave this question later.
> A last (but not least) question: I installed gromacs on my Debian
> Testing laptop; how do I run the examples/tutorials?
GROMACS works almost with command-line tools so you need to open the 
terminal windows to type commands inside them. So get yourself with some 
basic Linux/Unix commands first if you are no so; then proceed with the 
tutorial.
> Is there any available gromacs code you recommend me to look at for my
> specific problem or as a good way to learn the ropes?
Check literature. I guess there would be some MD work done on your 
topic. You may then migrate them to GROMACS by looking at them. You may 
raise relevant question to this list.

However, if you are doing Langevin dynamics of non-atomistic models, you 
may get easier life with Espresso than GROMACS.
www.*espresso*.mpg.de
> Many thanks
>
> Lorenzo
>
>
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