This file is part of the supporting data for the manuscript 
    Jerelle A. Joseph, Aleks Reinhardt, Anne Aguirre, Pin Yu Chew, Kieran O. Russell, Jorge R. Espinosa, Adiran Garaizar, Rosana Collepardo-Guevara, 'Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy', Nat. Comput. Sci. (2021).

Here we include the code necessary to obtain the results in the paper.

The majority of the code requires a compiled version of Lammps. We used the 10 March 2021 version for these calculations running on Linux (kernel 3.10.0) with standard libraries.

The code in the fig2-PMF directory requires Gromacs 4.5 instead.

There are five directories in this archive. Four of these correspond to figures in the results section of the manuscript, and each one contains a separate README file detailing its contents.

The final directory, 'all-model-parameters', contains Lammps parameter files not only for the Mpipi potential, but also for all the other models we have benchmarked. These parameter files can be used instead of the Mpipi parameters in the simulations provided in the other directories.



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Step-by-step guide to reproducing the example simulation data
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We assume here a standard Linux environment with basic tools, such as a compiler, already installed. A '$' at the start of a line implies the command should be run in a terminal.
Instructions on how to compile Lammps are provided at https://docs.lammps.org/Build_make.html, and vary slightly depending on the operating system used. We outline an example of the entire procedure below.

1. In a clean directory, download Lammps:
$ wget https://github.com/lammps/lammps/archive/refs/tags/patch_10Mar2021.tar.gz

2. Uncompress it:
$ tar zxf patch_10Mar2021.tar.gz

3. Compile it. When compiling Lammps, to enable the Wang-Frenkel potential, use 'make yes-USER-MISC' [or, if compiling with more recent versions of Lammps, 'make yes-EXTRA-PAIR'] before running 'make mpi' or 'make serial' (depending on whether parallelisation is desired). Other options may be needed if, for example, compiling with the Intel compilers.

$ cd lammps-patch_10Mar2021/src/
$ make yes-USER-MISC
$ make yes-MOLECULE
$ make serial

4. Once compilation is complete, depending on the options chosen, a binary such as 'lmp_serial' will be produced. Change to one of the example directories provided in this archive. For example:
$ cd PATH/TO/UNCOMPRRESSED/ARCHIVE/fig5-phase-diagrams/example-simulation

5. Run the simulation. [If Lammps was compiled with MPI enabled, an analogous command can be run through mpirun.]
$ PATH/TO/COMPILED/LAMMPS/lmp_serial -echo none -screen none -in input-script.dat


6. In order to generate results for other temperatures or input files (e.g. for other variants), the relevant lines in the input-script.dat file (and its equivalents in other directories) can straightforwardly be edited.