Clathrin Assembly Tutorial

1. Obtaining input files

In order to start a new simulation, you need a parameter file with .inp extension, and all .mol file required by that parameter file. mol files specify the structure of specific molecule, including the location of all its interfaces, and both translational and rotational diffusion constants. inp files control reaction rules as well as simulation settings. (see Input and Output file section in the user guide for more info)

A full set of sample input files for this simulation is provided:

• Click to download the sample input files

clat.mol
ap2.mol
pip2.mol
parms.inp
parmsMacroRate.inp // alternative parameter file with macroscopic rates

2. Running simulations

Once you have the input files and the compiled executable nerdss file in the sample directory, you can run the simulation using the following command:

./nerdss -f parms.inp > log.txt

If nerdss is compiled correctly, the simulation should be running and the text outputs should be recorded in log.txt.

3. Getting the outputs

After the simulation is completed, you can find the output files in the same directory. NERDSS generates several output files that records many aspects of the system during the simulation including copy numbers of every molecule, numbers of bonds and complexes formed, and location of each molecule during the simulation time. More details on the different output files generated by NERDSS and the types of data that they record can be found in the NERDSS user guide. Users can obtain their perferred information from the output files. For example, here is a demonstration of an animation of the clathrin simulation generated using the PDB files outputted by NERDSS:

Some useful helper functions to analyze the NERDSS output files are included in our ioNERDSS package. Intructions for downloading and using ioNERDSS can be found in more details in the ioNERDSS user guide.