update README.md

README.md

@@ -1,13 +1,5 @@
 # `COSMO`: COarse-grained Simulation of intrinsically disordered prOteins with openMM 
 
--------------------------------------
-<b>Package under refactoring</b>:
-- Initially, the package was named `hpsOpenMM` because it used the hps scale to simulate IDP. 
-However, we are now implementing more models, such as mpipi, which do not use the hps scale anymore. 
-Therefore, a different name is needed. We decided to change the name to `cosmo`.
-
-- If the name `hpsOpenMM` still appears in the documentation/source code, it means that we missed some instances of 
-renaming.
 -------------------------------------
 ### A coarse-grained simulation engine empowered by openMM
 
@@ -20,7 +12,7 @@ Currently, there are four models are supported:
 4) `mpipi`: another model that using Wang-Frenkel short range potential instead of LJ 12-6
 5) Other models can be easily implemented by defining them in `cosmo/parameters/model_parameters.py`
 
-Model summary
+<u>Models summary:</u>
 -------------
 | Model      | components support                    | Implemented             | Tested  |
 |------------|---------------------------------------|-------------------------|---------|
@@ -145,23 +137,23 @@ minimize = yes ;if not restart, then minimize will be loaded, otherwise, minimiz
 
 ## Bugs
 
-- If you encounter any bugs, please report the issue to Quyen Vu (`vuqv.phys@gmail.com`). 
+- If you encounter any bugs, please report the issue to `Quyen Vu` (`vuqv.phys@gmail.com`). 
 - Please note that any bugs encountered are my responsibility and not that of the authors of the models. 
 Therefore, I kindly request that you refrain from bothering them regarding any issues that may arise.
 
-## Acknowledgments
+## <u>Acknowledgments:</u>
 
 
-## Cite this work
+## <u>Cite this work</u>
 
 This software is based on the original work of Prof. Jeetain Mittal's group (hps family) and 
 Prof. Rosana Collepardo-Guevara's group (mpipi model). We have not published any paper using this software yet. 
 If you have used it in your publications, please cite the source accordingly.
 
-* hps family:
+* `hps` family (`hps-urry`, `hps-kr`, and `hps-ss`):
   - (`hps-kr`) Dignon, G. L.; Zheng, W.; Kim, Y. C.; Best, R. B.; Mittal, J. Sequence Determinants of Protein Phase Behavior from a Coarse-Grained Model. PLoS Comput. Biol. 2018, 1–23. https://doi.org/10.1101/238170.
   - (`hps-urry`) Regy, R. M.; Thompson, J.; Kim, Y. C.; Mittal, J. Improved Coarse-Grained Model for Studying Sequence Dependent Phase Separation of Disordered Proteins. Protein Sci. 2021, 30 (7), 1371–1379. https://doi.org/10.1002/pro.4094.
   - (`hps-ss`) Rizuan, A.; Jovic, N.; Phan, T. M.; Kim, Y. C.; Mittal, J. Developing Bonded Potentials for a Coarse-Grained Model of Intrinsically Disordered Proteins. J. Chem. Inf. Model. 2022, 62 (18), 4474–4485. https://doi.org/10.1021/acs.jcim.2c00450.
 
-* mpipi
+* `mpipi`
   - (`mpipi`)  Joseph, J. A.; Reinhardt, A.; Aguirre, A.; Chew, P. Y.; Russell, K. O.; Espinosa, J. R.; Garaizar, A.; Collepardo-Guevara, R. Physics-Driven Coarse-Grained Model for Biomolecular Phase Separation with near-Quantitative Accuracy. Nat. Comput. Sci. 2021, 1 (11), 732–743. https://doi.org/10.1038/s43588-021-00155-3.