Updated README.md; Changed file names and entry points

wehs7661 · Oct 25, 2023 · 2f4c0c7 · 2f4c0c7
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diff --git a/README.md b/README.md
@@ -12,7 +12,7 @@ Ensemble Molecular Dynamics
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-**ensemble_md** is a Python package that provides methods for setting up, running, and analyzing molecular dynamics ensembles in GROMACS. The current implementation is mainly for synchronous ensemble of expanded ensemble (EXEE), but we will develop methods like asynchronous EEXE, or ensemble of alchemical metadynamics in the future. For installation instructions, theory overview, tutorials, and API references, please visit the [documentation](https://ensemble-md.readthedocs.io/en/latest/?badge=latest).
+**ensemble_md** is a Python package that provides methods for setting up, running, and analyzing molecular dynamics ensembles in GROMACS. The current implementation is mainly for synchronous replica exchange (REX) of expanded ensemble (EE), abbreviated as REXEE. In the future, we will develop methods like asynchronous REXEE or multi-topology REXEE. For installation instructions, theory overview, tutorials, and API references, please visit the [documentation](https://ensemble-md.readthedocs.io/en/latest/?badge=latest).
 
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diff --git a/ensemble_md/cli/analyze_EEXE.py → ensemble_md/cli/analyze_REXEE.py b/ensemble_md/cli/analyze_EEXE.py → ensemble_md/cli/analyze_REXEE.py
diff --git a/ensemble_md/cli/explore_EEXE.py → ensemble_md/cli/explore_REXEE.py b/ensemble_md/cli/explore_EEXE.py → ensemble_md/cli/explore_REXEE.py
diff --git a/ensemble_md/cli/run_EEXE.py → ensemble_md/cli/run_REXEE.py b/ensemble_md/cli/run_EEXE.py → ensemble_md/cli/run_REXEE.py