The general steps of running Asynchronous wepy are:
Although there is deprecated code to run asynchronous wepy with molecular complexes and many-dimensional random walks, it currently works only with 1-D random walks.
Note: Changes were made to wepy files to facilitate this project. The wepy repository used is stored at /dickson/s2/jim/repos/wepy
on Markov. Within the wepy repo, the modified files are:
The example below will run Async. wepy with a system that is a 1-D random walk with 40 states. When selecting states for additional sampling, the async. methods will select 3 positions and 3 frames within each position. A trajectory starting from each state will be simulated once.
Running pipeline.py
with the argument -h
will print the help menu detailing the available arguments. Some of the arguments are:
%%bash
conda init bash
conda activate /dickson/s2/jim/bin/miniconda3/envs/openmm_env3
python /dickson/s2/jim/repos/wepy_async/pipeline.py \
-i /dickson/s2/jim/repos/wepy_async/simulations/testing/random_walk/revo/p_min_1E-12/50_runs_10k_cycles/forward_prob_0.3476700000000077/simulations/wepy_pre-revo-merge \
-o ~/async_wepy_example \
-c 40 \
--max_cycles 20 \
--committors /dickson/s2/jim/repos/wepy_async/committors_r_0.3476700000000077.txt \
--min_committor 0.5 \
--states 40 \
--prob_file /dickson/s2/jim/repos/wepy_async/forward_prob_peaked.txt \
--n_async_clusters 3 \
--n_async_frames_per_cluster 3 \
--n_async_reps 1 \
--debugging \
--testing
no change /dickson/s2/jim/bin/miniconda3/condabin/conda no change /dickson/s2/jim/bin/miniconda3/bin/conda no change /dickson/s2/jim/bin/miniconda3/bin/conda-env no change /dickson/s2/jim/bin/miniconda3/bin/activate no change /dickson/s2/jim/bin/miniconda3/bin/deactivate no change /dickson/s2/jim/bin/miniconda3/etc/profile.d/conda.sh no change /dickson/s2/jim/bin/miniconda3/etc/fish/conf.d/conda.fish no change /dickson/s2/jim/bin/miniconda3/shell/condabin/Conda.psm1 no change /dickson/s2/jim/bin/miniconda3/shell/condabin/conda-hook.ps1 no change /dickson/s2/jim/bin/miniconda3/lib/python3.9/site-packages/xontrib/conda.xsh no change /dickson/s2/jim/bin/miniconda3/etc/profile.d/conda.csh no change /home/jim/.bashrc No action taken. Starting at 2022-09-07 11:55:56.499192 Run finished