LAMMPS simulations of intrinsically disordered region (IDR) polymers with stickers under various conditions. Includes equilibration, osmotic pressure measurements, and client protein interactions.
LAMMPS equilibration and production runs of IDR polymer systems (Chain450 with 58 stickers) and compact spacer polymers under confinement.
File locations:
- Compact spacers:
simulations_fig2_fig3/compact_spacers/ - IDR spacers:
simulations_fig2_fig3/idr_spacers/
Run MATLAB scripts to generate initial configurations, then run LAMMPS input files in each directory.
Pressure measurements of IDR polymers at different volume fractions (vf=0.29-0.79). Used to calculate osmotic pressure and phase behavior.
File locations:
- Initial configurations:
simulations_fig4/initial_vf${vf}/polymer_system_vf${vf}_rep1.data - Input script:
simulations_fig4/input_script.in
Generate initial configurations:
cd simulations_fig4
module load anaconda
python initial_generator.py
Run simulation:
mpirun -np 48 lmp -in input_script.in -var replica <rep> -var volume_fraction <vf>
Output: simulations_fig4/pressure_vf${vf}/pressure_vf${vf}_rep${replica}.txt
IDR polymers interacting with point client particles at variable interaction strengths (epsilon=1-10). Density profiles characterize polymer partitioning.
File locations:
- Initial configurations:
simulations_fig5/initials/Sticker58_Chain450_NP50_Particle50_Rep${index}.initial - Input script:
simulations_fig5/input_script.in - Interaction tables:
simulations_fig5/tables3.dat
Run simulation:
mpirun -np 48 lmp -in simulations_fig5/input_script.in -var index_arg <replica> -var epsilon_value <eps>
Arguments:
index_arg: Replica number (1-30)epsilon_value: Interaction strength (1-10)
Output:
- Density profiles:
simulations_fig5/Out_profile/density_clients_eps${eps}_rep${replica}.dat - Trajectories:
simulations_fig5/OutC/FULL_trajectory_clients_eps${eps}_rep${replica}.xyz
Analysis: python simulations_fig5/plot_profiles.py or python simulations_fig5/extract_Kd.py