sulcgroup / anm-oxdna

oxDNA/oxRNA code that implements Anisotropic Network Model representation of proteins, allowing for simulations of hybrid protein-DNA/RNA nanostructures as well as biological complexes on CPU and GPU

Oxdna with DNA/RNA - Protein Hybrid Models

An extension of the oxDNA/RNA models that also includes Anisotropic Network Model for representation of proteins. Included in the repository is the simulation code in the oxDNA directory as well as the scripts for generating peptides/proteins with examples. Examples of setting up a simulation of protein (represented using ANM model, or ANMT model) with oxDNA or oxRNA, along with the necessary conversion scripts, are provided in ANMUtils directory.

An overview of the models is provided in the manuscript as well as in documentation online.

Models

Below are the Interaction Types for protein and DNA/RNA - protein hybrid simulations along with a brief description of their purpose. The models are specified as interaction_type in the input file. The respective interaction types are discussed in the documentation and include:

• AC -> For Simulation of Proteins exclusively, Treats the system as the classic ANM
• ACT -> For Simulation of Proteins exclusively, Uses classic ANM and bending/torsional modulation
• DNANM -> For Simulation of Proteins and DNA, Uses classic ANM for protein and oxDNA2 for DNA
• DNACT -> For Simulation of Proteins and DNA, Uses ANMT model for protein and oxDNA2 for DNA
• RNANM -> For Simulation of Proteins and RNA, Uses classic ANM for protein and oxRNA2 for RNA
• RNACT -> For Simulation of Proteins and RNA, Uses ANMT model for protein and oxRNA2 for RNA

Documentation

Basic Documentation relating to file formats (.top, .par, .dat, and input) can be found in documentation and their genration from PDB file are provided in ANMUtils directory.

Example Usage of the model with the provided scripts is shown in a series of example Jupyter Notebooks that are designed as walk-through of settign up simulation files and model parameters, as well as running simulations of the respective systems.

Citation

If you use the ANM-oxDNA model, we would appreciate if you can cite the following article: J Procyk, E Poppleton, P Šulc: Coarse-Grained Nucleic Acid-Protein Model for Hybrid Nanotechnology - arXiv preprint arXiv:2009.09589, 2020

anm-oxdna's Issues

CUDA max_density_multiplier issue from oxDNA

Hi,

I have encountered the same issue mentioned here in anm-oxdna too when I simulate in RNACT mode and when multiple proteins and RNAs are involved.

error CUDA

hi.
I got below error while installing anmoxDNA with CUDA

Please guide me to fix the error

[ 94%] Building NVCC (Device) object src/CMakeFiles/oxDNA.dir/CUDA/Thermostats/oxDNA_generated_CUDASRDThermostat.cu.o
/home/hadi/Downloads/anm-oxdna-master/oxDNA/src/CUDA/Lists/CUDASimpleVerletList.cu(155): error: identifier "cudaBindTexture" is undefined

/home/hadi/Downloads/anm-oxdna-master/oxDNA/src/CUDA/Lists/CUDASimpleVerletList.cu(182): error: identifier "cudaUnbindTexture" is undefined

5 errors detected in the compilation of "/home/hadi/Downloads/anm-oxdna-master/oxDNA/src/CUDA/Lists/CUDASimpleVerletList.cu".
CMake Error at oxDNA_generated_CUDASimpleVerletList.cu.o.Release.cmake:280 (message):
Error generating file
/home/hadi/Downloads/anm-oxdna-master/oxDNA/build/src/CMakeFiles/oxDNA.dir/CUDA/Lists/./oxDNA_generated_CUDASimpleVerletList.cu.o

make[2]: *** [src/CMakeFiles/oxDNA.dir/build.make:217: src/CMakeFiles/oxDNA.dir/CUDA/Lists/oxDNA_generated_CUDASimpleVerletList.cu.o] Error 1

Compilation instructions

Sorry if it's included somewhere, but I can't find any compilation instructions. I struggled a bit to get the correct combination of gcc/cuda for it to compile - gcc 7.3.0 and cuda 10.2 works for me, and I needed to enable c++11 in cmake as well. Hope this can be specified somewhere in the docs/readme.