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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