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HP1paralogs-simulations

Scripts to run the simulations of HP1 paralogs

3D structures

The PDB_files folder contains all the PDB files used for the simulations in the paper (e.g., HP1 homo- and heterodimer, chimeras, ...).

Single-chain simulations

  1. All-atom simulations

The AA_sim folder contains the Amber99SBws-STQ force field and sample script to run an all-atom simulation of $\rm HP1\alpha$ homodimer using OpenMM (7.5.1).

# 50ns equilibration.
python run_equilibration.py -t 50 -f hp1a_dimer_amber99sbws_stq_tip4p2005s

# 350ns production from checkpoint.
python run_omm.py -t 50 -f hp1a_dimer_amber99sbws_stq_tip4p2005s  -idx1 1 -idx2 2
  1. Coarse-grained simulations

Sample scripts in the CG_sim folder are used to run the single-chain coarse-grained simulation of $\rm HP1\alpha$ homodimer in LAMMPS.

mpirun lmp_mpi -in hp1a.lmp > log.out

Coarse-grained phase coexistence simulations

Sample scripts in the CG_slab_sim folder are used to run the coarse-grained slab simulation of $\rm HP1\alpha$ homodimer in HOOMD.

python run_nvt.py 170x170x170_box_min.gsd --mode=gpu

Note

HOOMD should be compiled with AZplugins https://github.com/mphowardlab/azplugins

Reference:

Phan et al., Interplay between charge distribution and DNA in shaping HP1 paralog phase separation and localization. (eLife 2024), https://doi.org/10.7554/eLife.90820