(Back to the AlgoSB Program page)

Modelling phase separation in the cell


The practical will cover the software and scripts necessary to use our coarse-grained modeling framework capable of providing molecular-level details on the sequence determinants of protein phase separation due to specific disease mutations and the inclusion of a folded domain, and variation of chain length.



HOOMD v2.9.7 installation with AZplugins:

More information regarding the installation can be found online:


To use short-range vdW interactions between amino acids we use azplugins which is a plugin for HOOMD-Blue.


Miniconda (https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html) can be used to install HOOMD prerequisites:


conda install -c conda-forge numpy cmake


Steps to compile HOOMD v2.9.7 with Azplugins (CPU):

mkdir HOOMD
cd HOOMD

# download source releases
wget https://glotzerlab.engin.umich.edu/Downloads/hoomd/hoomd-v2.9.7.tar.gz
wget https://github.com/mphowardlab/azplugins//archive/master.zip

# unzip downloaded files

tar -xvf hoomd-v2.9.7.tar.gz

unzip master.zip && mv azplugins-main/ azplugins

# to build azplugins internally to HOOMD-blue:

# add a symlink to the code into the hoomd-blue/hoomd:

cd hoomd-v2.9.7/hoomd

ln -s ../../azplugins/azplugins azplugins

cd ../


# Configure and compile

mkdir build

mkdir exec

p=$PWD
build_prefix=$p/build
install_prefix=$p/exec
cd $build_prefix
cmake .. -DCMAKE_INSTALL_PREFIX=$install_prefix -DCMAKE_BUILD_TYPE=Release -DSINGLE_PRECISION=ON -DBUILD_HPMC=OFF -DBUILD_CGCMM=OFF -DBUILD_DEM=OFF -DBUILD_DEPRECATED=ON -DBUILD_MD=ON -DBUILD_METAL=OFF -DBUILD_TESTING=ON -DBUILD_VALIDATION=OFF -DENABLE_MPI_CUDA=OFF -DENABLE_HPMC_MIXED_PRECISION=OFF


make
make install



Put the directory in which build files have been written to your ~/.bashrc:

export PYTHONPATH=$PYTHONPATH:~/HOOMD/hoomd-v2.9.7/build


source ~/.bashrc



To install GPU-supported version, you need: NVIDIA CUDA Toolkit >= 9.0

Specify -DENABLE_CUDA=ON to compile code for the GPU (requires CUDA) and -DENABLE_MPI=ON to enable parallel simulations with MPI.


HOOMD 2.9.7 installation using conda (CPU-only, w/o AZplugins):


Install Miniconda: https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html


conda create --name py_hoomd python=3.7
source activate py_hoomd
conda install -c conda-forge "hoomd=2.9.7=*cpu*"



Other dependencies required for tutorial:

conda install -c conda-forge notebook
conda install -c conda-forge fresnel
pip install gsd
pip install matplotlib