wlcsim 0.1.3

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What is wlcsim?

A project started by the Spakowitz lab for carrying out various polymer physics calculations, especially multi-scale, coarse-grained simulation and theory relating to semiflexible polymers. The library has been applied largely to simulate DNA, and to compare results from polymer field theory to measurements of biological polymer systems, but our universal coarse graining procedure and our field theoretic results should be broadly applicable to any semiflexible polymer system.

For example, combining our coarse graining procedure with field theoretic simulations, we were able to simulate the phase segregation of an entire chromosome due to H3K9 methylation.

There are two largely independent codebases that are each called wlcsim. One is a Fortran program that implements our universal coarse graining procedure to allow Monte Carlo and Brownian dynamics simulations of semiflexible polymers with high discretization lengths (i.e. with a very small number of beads). The Monte Carlo routines in this codebase are highly optimized, and integrated with our field theoretic simulations. For details see wlcsimf.

There is an associated Python package, wlcsim, which can be used to help process the output of our Fortran code, but also contains much easier to use Monte Carlo and Brownian dynamics routines. For more details on this package, see the wlcsimpy docs.

The remainder of this section focusus on the FORTRAN code. The features of this codebase are described in features.

Setting up a Fortran simulation

To define the system you would like to simulate, set the approparte values src/defines.inc. Discriptions of each parameter are found along with their definitions in src/defines.inc. In pracatice, the best approach is often to start from examples provided in input/example_defines/.

Some parameters that MUST be set are given default values that prevent the code from compiling. This is on purpose so that the code is not accidentally run with something arbitrary for these values (like the length of the chain, the persistence length, etc).

For tips on setting up and running simulations see tips.

Running the Fortran code

Simply typing make in the top level directory will build the simulator from source. The executable created (wlcsim.exe) will data from the input/ directoyr and write its output to the data directory. To force a rerun without having to manually delete all the old output files, you can also simply type make run at any time.

By default, specifying multiple polymers just simulates them in parallel in the same reaction volume, no interactions are assumed.

To scan parameters, the Python script scan_wlcsim.py should be used. It takes care of saving the current git commit_hash, all inputs, etc. into a unique directory, and preventing race conditions even on shared filesystems, among other things.

To perform parallel tempering using MPI for multiprocessing using 10 threads first compile using make then type mpirun -np 10 wlcsim.exe. For more details on parallel tempering see parallel_temp.

Output

There are several ways to easily visualize simulation output. There are PyMol scripts in the vizualization directory, python -m wlcsim.plot_wlcsim from the repo’s top level directory will launch a GUI designed to visualize BD simulations, and one can of course simply use the output in the data directory, which contains rank two arrays of shape num_beads*num_polymers-by-3, with one file per time point.

For more details see output.

Disclaimer

This codebase is internal to the Spakowitz lab and is not guaranteed to be bug-free at any point. For battle-tested versions of our software, please see the links in the relevant papers.