Running examples with GPU using docker container.

docker/README.md

@@ -39,3 +39,23 @@ All differences are within tolerance.
 ```
 Note: `perses` currently works best on a single GPU. 
 See the documentation [here](https://docs.docker.com/config/containers/resource_constraints/#access-an-nvidia-gpu) for how to specify a single GPU on a multi-GPU system.
+
+## Running perses examples from the container in GPUs using CUDA
+
+If you plan to use our docker container and CUDA/GPUs, quick instructions to get the examples running are as follows.
+
+We have our examples with minimalistic setups to satisfy our current continuous integration (CI) workflow. To get more "realistic" simulations I recommend making the following modifications.
+
+1) Clone our repository (say it lives in `$HOME/repos/perses`)
+
+2) Modify the `run_neq_distrib_flattened.py` inside each of the examples you want to run:
+- Change the platform name to 'CUDA '(it is CPU by default to satisfy our continuous integration). Should be in line 21 in the script.
+- (recommended) You might want to change the nsteps_eq and nsteps_neq (number of steps for equilibrium and nonequilibrium, respectively) to a larger value. Something around 250000 steps (1ns in time) for each should be okay. These should be lines 17 and 18 in the scripts.
+- (recommended) Please change the save frequency or else you would be storing A LOT! I guess the actual value depends on what you actually want to see, but please do change it if you increase the number of steps as in the previous item.
+
+3) Run our latest docker container and execute an example.
+    For example for the kinase-neq-switching example, you would do something like:
+```bash
+docker run -it --rm --gpus device=0 --mount type=bind,source=$HOME/.OpenEye/,target=/openeye/,readonly --mount type=bind,source=$HOME/repos/perses/examples/,target=/mnt/ -w /mnt/kinase-neq-switching choderalab/perses:0.9.2  python run_neq_distrib_flattened.py
+ ```
+Of importance there are the paths to the OpenEye license file (in this example is `$HOME/.OpenEye/`), path to the examples directory in perses (`$HOME/repos/perses/examples/`) and the actual example subdirectory example you want to run (`/mnt/kinase-neq-switching`)