cytosim for 3D actomyosin simulations¶
Cytosim is a nice, well tested simulation software for cytoskeleton mechanics. This is only a short summary on the steps you have to perform to get cytosim up and running for the simulations we do. Look for the documentation on their project page for more details.
Compile¶
Instead of following their default instructions, which would create cytosim executables for 2D simulations, use
make bin3/sim
make bin3/play
make bin3/report
This will put the executables into the folder bin3.
Install¶
Now that the program is built, you need to install it. It’s not strictly necessary, but I
find it much more convenient. Installing a program for command line is equivalent to adding
the executable file to your so called PATH. The PATH is a list of directories,
in which your command line is searching for executable files.
One option you have, is to permanently add the folder bin3 to your PATH. For that, find out
what the absolute path to the folder bin3 is. You could for example use the command pwd, which
gives you the absolute path to the folder where you currently are in your command line session. Mine
e.g. would yield /home/ilyas/Software/cytosim. So the absolute path to the bin3 folder which
contains the executables is
/home/ilyas/Software/cytosim/bin3
in my case. To add that permanently to your PATH, you need to add one line to the file
~/.bashrc. The ~ is a short cut to your home folder, in my case that would be /home/ilyas.
The file .bashrc starts with a dot, which means that it is ignored by many programs, and
is considered a hidden file for most file browsers. So don’t worry if you don’t see it,
it should be there on most Linux machines. You have to add the line
export PATH=$PATH:/home/ilyas/Software/cytosim/bin3
This sets the new list PATH to contain the old list plus the bin3 folder.
Replace the path where it is located on my machine (/home/ilyas/...) with whereever it
is on yours.
Learn cytosim¶
I found that most tutorials also work in 3D, even though they were designed to run in 2D. After the introductory tutorial you should continue with the tutorials on actin, e.g. this one.
3D Simulation Box with Periodic Boundaries¶
In our lab, we often use a box instead of spheres/cells or similar shapes from the tutorials. For example:
set space box {
shape = periodic
}
new box {
length = 30, 30, 30
}
If you also use a periodic box, make sure you set all lengths of couples to 0.
Otherwise cytosim will produce an error, if a couple crosses a periodic boundary.