Split Mfp5 Simulations

Instructions to generate and run simulations presented in J. Graham and S. Keten "Increase in charge and density improves strength and toughness of mfp5 inspired protein materials" ACS Biomaterials Science and Engineering 2023

If you use this tool, please cite the above paper.

Employed Software Version Histories:

• LAMMPS version used is from March 3, 2020 downloadable here: https://download.lammps.org/tars/index.html

• Packmol version 20.1.1 was used. Download and instructions for Packmol can be found here: https://m3g.github.io/packmol/

• Conda version 4.10.3

• Anaconda version 4.3.0

• Python version 3.6.0

• VMD version 1.9.3

• perl v5.16.3

• GNU Bash, version 4.2.46(2)-release (x86_64-redhat-linux-gnu)

File Descriptions:

In main directory Split_Mfp5_Simulations

• chloride.pdb - PDB file for a chloride ion with arbitrary coordinates assigned.

• fga_fp5.yml - Conda .yml file, which can be used to create an environment compatible with scripts written for this project.

• multiLooseChainGenerator.py - Takes as input a text file with no spaces made up of the one letter shorthand for common amino acids and generates a pdb for a linear protein chain with random dihedral angles restricted between 120 and 240 degrees.

• psfgen.tcl - Generates psf, pdb, and per files of the protein melt system with all protein, water, and ions using VMD's psfgen plugin.

• sodium.pdb - PDB file for a sodium ion with arbitrary coordinates assigned.

• splitpdbforpsfgen-addsegID.py - Splits the pdb file entitled 'chains_packed.pdb' into pdb files of each individual chain and water/ions. Output files are melt_ions.pdb, melt_water.pdb, and melt_chain{1...numchains}.pdb. This is necessary to use the VMD psfgen plugin.

• • water.pdb - PDB file for a water molecule with arbitrary coordinates assigned.

• submit.sh - A bash script documenting the entire workflow to build simulations in Graham et al., ACS Biomaterials Science and Engineering, 2023.

Instructions:

1. Create a conda environment from fga_fp5.yml in a location of your choosing using instructions found in [conda documentation] (https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-from-an-environment-yml-file).

2. Download packmol in a location of your choosing.

3. Ensure all software versions being used are correct.

4. File submit.sh contains all the bash commands necessary to build simulations and can be run using the command "bash submit.sh". Before running submit.sh, there are a few lines of code that must be changed. 1) Change the line "source activate /projects/p31412/Mfp_Brushes/envs/fga_mfp" such that it specifies the path to your newly created conda environment. 2) Correct the line "/home/jjg9482/packmol/packmol < pack1_chains.inp" such that the command specifies the path to your newly installed packmol executable. Keep '< pack1_chains.inp' after you have specified the path. This indicates which packmol input file to use. 3) Change the commands "module load python/anaconda3.6" and "module load vmd" to specify paths to your pre-compiled versions of anaconda and vmd. 4) Run the script using "bash submit.sh"

5. Change directories into the newly generated directory containing all simulations entitled split_fp_simulations and navigate into the directory annealing_input_submit. split_fp_simulations is outside of the directory Split_Mfp5_Simulations. Run the bash script copy_lmpin.sh using "bash copy_lmpin.sh", which will modify annealing_template.in and copy it as annealing.in into the annealing directory of each simulation.

6. Run the bash script copy_submit.sh using "bash copy_submit.sh", which will modify submit_annealing_template.sh and copy it as submit_annealing.sh into the annealing directory of each simulation.

7. Navigate into each simulation's annealing directory and submit them using the commands in submit_annealing.sh. Note that the mpirun command executes a parallelizable version of lammps and there are a number of settings passed by #SBATCH specifying batch job details which will vary by computing cluster. Alternatively, submit_all_annealing.sh has been copied into split_fp_simulations, which navigates into each directory and runs the bash commands found in submit_annealing.sh using sbatch.

8. Once the simulations are complete, navigate into the directory tensile_input_submit and run copy_lmpin.sh, which will modify tensile_test_template.in and copy it as tensile_test.in into the tensile_test directory of each simulation. This script also copies the final data file 7_T300_P1.data output by annealing.in into tensile_test so that the simulation can contain from the equilibrium configuration.

9. Run the bash script copy_submit.sh, which will modify submit_tensile_test_template.sh and copy it as submit_tensile_test.sh into the tensile_test directory of each simulation.

10. Navigate into each simulation's tensile_test directory and submit them using the commands in submit_tensile_test.sh. Note that the mpirun command executes a parallelizable version of lammps and there are a number of settings passed by #SBATCH specifying batch job details which will vary by computing cluster. Alternatively, submit_all_tensile.sh has been copied into split_fp_simulations, which navigates into each directory and runs the bash commands found in submit_tensile.sh using sbatch.