md_patchy_model

Tutorial on using the MD Patch Model of JR Espinosa et al.

 In case of problems please email: jaj52@cam.ac.uk

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Reference

If you use any of this code please cite the reference below, which includes full details on the model:

J. Chem. Phys. 150, 224510 (2019) https://aip.scitation.org/doi/10.1063/1.5098551?af=R&

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Software and Packages

1. LAMMPS (Large-scale atomiic/molecular massively parallel simulator)

   1.1. Install LAMMPS with mpi - for more information on how to obtain and install LAMMPS see: https://lammps.sandia.gov/doc/Install.html

   1.2. Example installation on HPC (Cambridge users)
   Download lammps source from github
   > git clone https://github.com/lammps/lammps.git
   > cd lammps
   > git checkout origin/stable
   > module purge
   > module load rhel7/default-peta4
   > cd src

   1.3. Install lammps packages (RIGID, USER-SMD, MOLECULE) required for MD patchy simulations
   > make yes-rigid
   > make yes-user-smd
   > make lib-smd args="-b"
   > make yes-molecule
   > make package-update
   > make mpi

   You should obtain the executable: lmp_mpi

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Procedure: MD simulation with patchy particles and polymer

We will prepare a box containing a given number of patchy particles (hard spheres with patches on them) and a polymer chain. Then we will simulate the system in the NVT ensemble. The following describes the files in each directory, in the order of usage.

STEP 1: replicate/
INPUT FILES

• conf1.xyz: xyz coordinates for one patchy particle in the correct format for lammps (ie input configuration)
• in.replicate: simulation parameters for replicating conf1.xyz. Gives a multiple of orginal patchy particle based on parameters given to "replicate" keyword
• table_gas_ideal.xvg: ideal gas potential for interactions between patches and hard spheres in tabular form
• table_PHS.xvg: potential for hard sphere-hard sphere interactions in tabular form
• table_12KT.xvg: potential for patchy-patchy interactions in tabular form

RUN AND USEFUL OUTPUT

• run.sh: example script for running lammps on the command line with the input files descried above
• replicas.lammpstrj: lammps trajectory file with given number of frames. Each frame will contain a box of many patchy particles (number of particles = xyz specified by replicate keyword)

STEP 2: removing_particles/

• replicas.lammpstrj: edited version of replicas.lammpstrj in which the last configuration is saved and all other configurations are discarded.
• trj_config: dumped coordinates from replicas.lammpstrj
• trj_ordered: atoms from trj_config sorted sequentially
• halo_bola.f90: selects a subset of particles between rmin and rmax from trj_ordered and formats coordinates
  Compile and run as follows:

gfortran -o halo_bola halo_bola.f90
./halo_bola

• boli_final.g96: formatted coordinates for subset (approx. 25%) of patchy particles obtained by compiling and running halo_bola.f90 above.

STEP 3: create_config/

• boli_final.g96: same as in step 2
• conf2.xyz: same format as conf1.xyz above. The number of atoms is updated to total in boli_final.g96 . The box information is obtained from replicas.lammpstrj. The last section of the file contains the contents of boli_final.g96. We now have a box containing 1584 patchy particles (equivalent to 6336 atoms).
• halo_chain.f90: Compile and run to set up atom coordinates, bonds and angles for polymer

gfortran -o halo_chain halo_chain.f90
./halo_chain

• chain.g96: formatted coordinates for polymer based on variables set in halo_chain.f90. Y and Z coordinates are edited manually for now.
• conf3.xyz: (cat conf2.xyz chain.g96 > conf3.xyz). Updated total atoms, bonds, angles. Updated atom types, bond types, angle types, added mass for polymer particles.

STEP 4: potentials/
The final step before we can run our simulations is to create the potentials for our patchy-particles and polymer chain interactions.

• Compile each file below with double precision

gfortran -fdefault-real-8 -o a.out ideal_gas.f
./a.out

• ideal_gas.f: produces table_gas_ideal.xvg which describes interactions between patches and hard spheres (atom types 1 and 2), and patches and polymer particles (2 and 3).
• potencial_LJ.f: produces table_LJ.xvg which describes interactions between hard spheres and polymer particles (atom types 1 and 3).
• potencial_PHS_lammps.f: produces table_PHS.xvg which describes interactions between hard spheres (1 and 1), and polymer particles (3 and 3)
• patch_patch.f: produces table_XKT.xvg which describes interactions between patches (2 and 2) at a given temparature.

STEP 5: simulate/

INPUT FILES

• conf3.xyz
• potentials in tabular form: table_gas_ideal.xvg, table_LJ.xvg, table_PHS.xvg, table_10_5KT.xvg
• in.minimal: lammps input file containing simulation parameters. A very short simulation.

RUN and OUTPUT

• run.sh: execute this script to obtain sample output.
• patchy_and_polymer.lammpstraj: Lammps trajectory file.

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Visualisation: (Optional)

• Load patchy_and_polymer.lammpstraj in VMD to visulalise box with polymer chain and patchy particles.