Atomic Resolution Brownian Dynamics (ARBD) - Nov 22

Brownian dynamics (BD) simulation is method for studying biomolecules, ions, and nanomaterials that balances detail with computational efficiency.

ARBD supports tabulated non-bonded and bonded interactions between BD particles that can also be influenced by grid-specified potentials. Uniquely, ARBD also allows grid-specified densities and potentials to be associated with rigid body particles that rotate and translate to represent larger molecules. Most importantly, the code is designed to run quickly on modern NVIDIA GPUs.

ARBD is a rewrite of the BrownianMover code, moving almost all computations to the GPU and enabling grid-specified particle models. Please be aware that ARBD is being actively developed and is offered without warranty.

Building

Dependencies

Only tested on Linux with:

• CMake >= 3.9
• gcc >= 4.9
• cuda >= 9.0

Build process

From the root arbd directory (where this README is found), run:

cmake -S src -B build &&
(
  cd build
  make -j
)

If your CUDA toolkit is installed in a nonstandard location that CMake is unable to find, you may provide use the environement variable CMAKE_CUDA_COMPILER to specify the path to nvcc. You may also find it neccesary to set the environment variable CUDA_INCLUDE_DIRS if compilation fails due to the compiler being unable to find <cuda.h>.

Note that ARBD has been developed using CUDA-9.0 and targets NVIDIA GPUs featuring 6.0 compute capability. The code should work with devices with compute capability >=2.0, but there are no guarantees.

Older versions of CUDA are not compatible with SM 6.0, so you may need to change the SMS variable in the makefile, or specify it as an argument to make.

Usage

Please explore the examples in the 'tests' directory.

For example, try the following commands:

cd tests/argon-small mkdir output ../../src/arbd BrownDyn.bd output/BrownDyn > output/BrownDyn.log

You may use the '-g n' option to specify the n-th GPU on your machine, counting from 0.

Citing

If you publish results obtained using ARBD, please cite the following manuscripts:

"DNA base-calling from a nanopore using a Viterbi algorithm" Winston Timp, Jeffrey Comer, and Aleksei Aksimentiev Biophys J 102(10) L37-9 (2012)

"Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics" Jeffrey Comer and Aleksei Aksimentiev. J Phys Chem C Nanomater Interfaces 116:3376-3393 (2012).

"Atoms-to-microns model for small solute transport through sticky nanochannels" Rogan Carr, Jeffrey Comer, Mark D. Ginsberg, and Aleksei Aksimentiev Lab Chip 11(22) 3766-73 (2011)

Authors

ARBD is developed by the Aksimentiev group (http://bionano.physics.illinois.edu) as a part of the NIH Center for Macromolecular Modeling and Bioinformatics (http://www.ks.uiuc.edu/).

Please direct questions or problems to Chris.

Christopher Maffeo cmaffeo2@illinois.edu Han-yi Chao Jeffrey Comer Max Belkin Emmanual Guzman Justin Dufresne Terrance Howard

Outstanding issues

• There are no checks to ensure that pairlists are recalculated before particles further than the pairlist distance move to within the cutoff

• A large amount of GPU memory for pairlists is allocated statically, which may cause out-of-memory crashes in older hardware