Self-Assembly

• wrap/wrap_trj.sh: trajectory wrapping using gromacs;

• cluster_size: calculate the number of cluster, maximum size of cluster, and L/D ratio;

• rdf: rdf analysis;

• sasa: solvent accessible surface area analsysis;

• order_param: order parameter analysis

## cal_order.sh
vmd -dispdev text -e order_v1.tcl -f ../../../model_construct/K4_0.15M_20_conc.gro -args ../product.??.wrap.xtc

• diffusion constant:

# utilizing gmx related commands
## combine multiple trajectories into one
gmx trjcat -cat -f [traj list] -o [name of combined traj] -settime -dt xxx
## calculate the MSD and estimate the $D$
gmx msd -f [path/to/combined traj] -s [path/to/topology] -o msdout.xvg -mol diff_mol.xvg

• num_density/num_density.tcl: calculate the num density of NA, CL, WATER

useage:
vmd -dispdev text -e num_density.tcl -f gro -args ../product.TOT.wrap.xtc

• dielectric constant

# create index.ndx file
gmx make_ndx -f tprfile/grofile -o index.ndx
# calculate the dielectric constant
gmx dipoles -f trjfiles -s tpr file -n index.ndx

• dipole_orient: Estimate the rot. degree of freedom

usage:
need to generate the charge info
gmx editconf -f tprfile -mead charge.pqr

• ene_decomp: Decompose interaction energies into Coulomb and LJ term using gromacs

just follow the page, make sure you have created correct index file and modify energygrps in mdp file

if you find these scripts useful for your research, please cite the following paper

@article{zhu2024understanding,
  title={Understanding and Fine Tuning the Propensity of ATP-Driven Liquid-Liquid Phase Separation with Oligolysine},
  author={Zhu, Qiang and Wu, Yongxian and Luo, Ray},
  year={2024}
}