SolventDynamics

SolventDynamics is an open-source code for computing accelerated non-adiabatic molecular dynamics by utilizing machine learning inferred energy and force vectors.

Installation

Python >= 3.7 torch >= 1.12 CUDA >= 11.6

To install:

• Create virtual environment

python -m venv ./solvent_venv
source ./solvent_venv/bin/activate

• Install CUDA 11.6

wget https://developer.download.nvidia.com/compute/cuda/11.6.0/local_installers/cuda-repo-rhel7-11-6-local-11.6.0_510.39.01-1.x86_64.rpm
sudo rpm -i cuda-repo-rhel7-11-6-local-11.6.0_510.39.01-1.x86_64.rpm
sudo yum clean all
sudo yum -y install nvidia-driver-latest-dkms cuda
sudo yum -y install cuda-drivers

• Install torch with CUDA

pip install torch --extra-index-url https://download.pytorch.org/whl/cu116

• Install torch - nightly build for vmap - with CUDA (optional)

pip install --pre torch torchvision torchaudio --extra-index-url https://download.pytorch.org/whl/nightly/cu116

• Install solvent from source:

git clone https://github.com/noahshinn/solvent.git
cd solvent
python setup.py develop

• Install solvent_namd from source by running:

git clone https://github.com/noahshinn/solvent-namd.git
cd solvent_namd
python setup.py develop

• Install the rest of the dependencies

pip install -r ./requirements.txt