Installation

TIES MD

TIES_MD can be installed with Conda on Linux-64 and Linux-ppc64le machines. The steps to do this are as follows, starting with an install of Miniconda:

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh -b -p $prefix
export PATH="$prefix/bin:$PATH"

Ensure the Miniconda used matches the platform on which you are running, for example use Miniconda3-latest-Linux-ppc64le.sh for Linux-ppc64le machines, and that $prefix is set to some directory with read write permissions. We provide Conda installs for Python 3.7/3.8/3.9 on Linux-64 and Python 3.7 on Linux-ppc64le. If required you can change your python version in Conda using this command:

conda install python=3.7.3

Finally add conda-forge to your available conda channels and install TIES MD:

conda config --add channels conda-forge
conda install -c adw62 ties_md

These install instructions are all that is needed to run TIES MD with NAMD. If you do not need OpenMM there is no need to read further.

TIES OpenMM

To use the OpenMM protocol in TIES_MD a custom version of OpenMMTools is needed to perform the alchemical transformations of the system and allow for thermodynamic integration calculations. In order to install the custom version of OpenMMTools run:

mkdir openmmtools_install
cd openmmtools_install
git clone -b adw62-PowerPC https://github.com/adw62/openmmtools.git
pip install ./openmmtools --use-feature=in-tree-build

The install of OpenMM which was installed with TIES_MD can be verified by running:

python -m openmm.testInstallation

for older OpenMM versions < 7.6 this command was:

python -m simtk.testInstallation

In some instances the wrong version of OpenMM and CUDAtoolkit could be installed this can be corrected by running:

conda install -c conda-forge openmm cudatoolkit=10.0

where 10.0 should be replaced with the particular CUDA version you want to target. See the OpenMM user guild for more details on this.

The install of TIES MD can be tested by downloading and running (Tutorial) any of the examples provided here. These examples can be download by running:

git clone https://github.com/UCL-CCS/TIES_MD.git