About

SOUFFLE is a molecular dynamics software for use in testing virus self-assemly with elastic capsomeres. Check out the Wiki for more detailed information!

Below are brief installation and run instructions.

NanoHUB app page:

• https://nanohub.org/tools/capsidsouffle

Install and run instructions on Cluster

• First, git clone the project: git clone https://github.com/softmaterialslab/capsid-souffle.git
• Then, load the required modules: boost, gsl and gnu computing environment.
• • These modules are installed for you in src/Makefile, currently configured for BigRed200 supercomputer module load gsl/2.8 && module load boost/1.86.0
• Next, go to the root directory: cd capsid-souffle
• Then, install the project: make cluster-install
• Submit an individual job: make cluster-submit
• Use parameter_sweep.sh to submit multiple jobs sweeping over a parameter ./parameter_sweep
• All outputs from the simulation will be stored in the bin folder when the simulation is completed.
• Check and compare files (ex: energy.out) inside the bin/outfiles directory; model.parameters.out contains info on the system.
• If you want to clean everything and create a new build, use: make clean
• If you want to clean the output data for a new run, use: make dataclean
• Submit a batch script or run with these boost option parameters: ./capsid-souffle -D b -f trimer_MVM -S 20 -d 100 -T 10000 -s 5000 -b 5000 -C 800 -c 100 -E 2.1 -t 0.005 -W 1000 -M 1000 -K 298

Install and run instructions on Local computer (Linux)

• Load the necessary modules: boost, gsl and openmpi module load gsl/2.8 && module load openmpi/3.0.1 && module load boost/1.86.0
• Also make sure to export OMP_NUM_THREADS environment variable with maximum threads available in your CPU: export OMP_NUM_THREADS=16
• Next, go to the root directory: cd capsid-souffle
• Then, install the project: make install
• Next, go to the bin directory: cd bin
• Next, run the job: time mpirun -np 1 -N 16 ./capsid-souffle -f trimer_MVM -S 20 -d 100 -T 10000 -s 5000 -b 5000 -C 800 -c 100 -E 2.1 -t 0.005 -W 1000 -M 1000 -K 298
• All outputs from the simulation will be stored in the bin folder when the simulation is completed.
• Check and compare files (ex: energy.out) inside the bin/outfiles directory; model.parameters.out contains info on the system.
• If you want to clean everything and create a new build, use: make clean
• If you want to clean the output data for a new run, use: make dataclean

Aditional information about different input parameter settings

• if testing on a separate folder, copy bin/infiles in addition to executable and job script