Versions¶
v0.1.1 Speed up updateParametersInContext¶
Create a new branch¶
# create a new branch and switch to it
git checkout -b 0.1.1_dev
# push the branch to github
git push -u origin 0.1.1_dev
# merge to master
git checkout master
git pull origin master
git merge 0.1.1_dev
git push origin master
Problem to be Solved¶
In the 0.1.0, updateParametersInContext cost ~1 min. This means if a RE/GCMC is accepted, the particular replica will spend 1 min waiting. There are two solutions to speed this up.
Solution Part 1: no configuration exchange in RE¶
In RE, if a move is accepted, the global parameter(s) in the MPI rank changes while the coordinate and velocity stay in the MPI rank. Only rank 0 collects and writes the trajectory/rst/energy.
By applying this, RE will only change the global parameter and will neither call set_ghost_list nor call updateParametersInContext.
Solution Part 2: split water-water into new CustomNonbondedForce¶
old |
core |
new |
fix |
wat |
Switch |
|
|---|---|---|---|---|---|---|
Old |
C1 |
|||||
Core |
C1 |
C1 |
||||
New |
None |
C1 |
C1 |
|||
Fix |
C1 |
C1 |
C1 |
C4 |
||
Wat |
C1 |
C1 |
C1 |
C3 |
C3 |
|
Switch |
C1 |
C1 |
C1 |
C2 |
C2 |
C2 |
C1 uses the same energy expression as before. The env group includes Fix and Wat, and the env-env intrection is now included in this CustomNonbondedForce.
C2 does not need to split state A and B in per particle parameter. It still need is_real and is_switch, the same as C1. It avoids the many global parameters which controls the RBFE and only includes lambda_gc_vdw and lambda_gc_coulomb for controlling the switching water
C3 only needs is_real, no global parameter
C4 does not change.
If water H has no vdw, remove them from the water group also speeds up the update. In this version, for the same HSP90 system, the time for updateParametersInContext is ~ 7s.
v0.1.0 Basic GC FEP functionalities¶
1. Documentation¶
1.1 Install Sphinx and autodoc extention¶
pip install sphinx sphinx-autodoc-typehints
mamba install ghp-import # for pushing doc to github
pip install --upgrade sphinx_mdinclude # for markdown support
1.2 Initialize Sphinx in the project¶
sphinx-quickstart docs
Edit docs/conf.py
make html
1.3 Push the documentation to gh-pages¶
ghp-import -n -p docs/_build/html
1.4 Check it online¶
2. set up pytest-mpi¶
conda install pytest-mpi
2.1 Run NPT RE test¶
mpirun -n 4 python -m pytest --with-mpi test/test_NPT_MPI.py
2.2 Run GC RE test¶
mpirun -n 4 python -m pytest --with-mpi test/test_GC_MPI.py::test_GC_RE
mpirun -n 8 --use-hwthread-cpus python -m pytest --with-mpi test/test_GC_MPI.py::test_GC_RE
# I only have 4 physical cores here.
