Improve the documentation of ensemble_md

[wehs7661]

This PR aims to address the todos listed in the section "Improving the documentation" in issue #41, which includes the following tasks:
- [ ] Update the theory section of the documentation
- [ ] Describe rules of thumb for REXEE parameters
- [ ] Proofread the entire documentation

• Proofread the docstrings

For a complete list of modules for docstrings proofreading, please visit issue #43.

[codecov]

Codecov Report

Attention: Patch coverage is 93.02326% with 3 lines in your changes are missing coverage. Please review.

Project coverage is 96.08%. Comparing base (27320da) to head (f6552e2).
Report is 1 commits behind head on master.

Files	Patch %	Lines
ensemble_md/analysis/analyze_matrix.py	87.50%	1 Missing ⚠️
ensemble_md/utils/gmx_parser.py	95.45%	1 Missing ⚠️
ensemble_md/utils/utils.py	50.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master      #46      +/-   ##
==========================================
- Coverage   96.10%   96.08%   -0.03%     
==========================================
  Files          10       10              
  Lines        1950     1914      -36     
==========================================
- Hits         1874     1839      -35     
+ Misses         76       75       -1     

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[wehs7661]

I renamed the branch from improve_docs to refine_docstrings as I wanted to divide up the tasks. Here I am reopening the PR change the branch being merged to the master branch.

[wehs7661]

Okay, it seems that changing the branch is not possible so I am going to open another new PR to include the work here. See Issue #48.