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