diff --git a/README.md b/README.md index 258dd3f1ed24b91ea48cfa746a788aba300f9d3e..fca3144ec9d7ad5848020de73332b6717a014f5f 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# Atomic Resolution Brownian Dynamics (ARBD) - Nov 22 +# Atomic Resolution Brownian Dynamics (ARBD) - May 24 Brownian dynamics (BD) simulation is method for studying biomolecules, ions, and nanomaterials that balances detail with computational @@ -21,15 +21,18 @@ offered without warranty. ### Dependencies -Only tested on Linux with: +Linux workstation with CUDA-compatible GPU (minimum 3.5 compute capability) - CMake >= 3.9 - gcc >= 4.9 - - cuda >= 9.0 + - cuda >= 9.0 (> 11.5 recommended) ### Build process From the root arbd directory (where this README is found), run: ``` +## Determine the compute capability of your CUDA-enabled graphics card +export CMAKE_CUDA_ARCHITECTURES="35;50;75;80" ;# especially important for CMake < 3.24.0 +## export CUDA_INCLUDE_DIRS="$CUDA_HOME/include" ;# optionally be explicit about cuda include paths; usually not needed cmake -S src -B build && ( cd build @@ -47,11 +50,6 @@ 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. @@ -70,35 +68,24 @@ counting from 0. 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/). +(http://bionano.physics.illinois.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 - +- Christopher Maffeo <cmaffeo2@illinois.edu> +- Han-yi Chao +- Jeffrey Comer +- Max Belkin +- Emmanual Guzman +- Justin Dufresne +- Terrance Howard ## Outstanding issues