polishing docs...

xBFreEnergy · Jul 8, 2023 · 74253db · 74253db
1 parent 2f619db
commit 74253db
Show file tree

Hide file tree

Showing 6 changed files with 33 additions and 66 deletions.
diff --git a/docs/apps.md b/docs/apps.md
@@ -9,10 +9,11 @@
         ![Image title](/assets/xbfree_logo.svg){ align=left width=400}
         </a>
 
-    xBFreE is a tool for calculating binding free energy. Although it is the natural evolution of gmx_MMPBSA to 
-    extend its functionalities to other MD programs, it also seeks to fulfill another objective. The idea behind the 
-    same-name project is to provide the scientific community with a robust tool that contains most of the most used 
-    BFE methods.  
+    xBFreE is a comprehensive tool designed for calculating binding free energies. While it builds upon the foundation 
+    of gmx_MMPBSA and aims to expand its capabilities to other molecular dynamics (MD) programs, it also serves an 
+    additional purpose. The underlying concept of the xBFreE project is to offer the scientific community a robust 
+    tool that encompasses a wide range of commonly utilized binding free energy (BFE) methods. Our goal is to provide 
+    researchers with a powerful and versatile resource to facilitate their investigations in this field. 
         
 
 ## xBFreE-Analyzer
@@ -24,5 +25,7 @@
         ![Image title](/assets/xbfree-ana_logo.svg){ align=left width=400}
         </a>
 
-    Like xBFreE, xBFreE-Analyzer arises from gmx_MMPBSA (gmx_MMPBSA_ana). xBFreE-Analyzer is a powerful graphical 
-    tool to carry out the analysis of the results obtained with xBFreE.
+    Similar to xBFreE, xBFreE-Analyzer is an extension of gmx_MMPBSA (specifically gmx_MMPBSA_ana). Serving as a 
+    robust graphical tool, xBFreE-Analyzer is designed to facilitate the analysis of results generated by xBFreE. 
+    Its powerful features enable researchers to effectively analyze and interpret the output obtained from xBFreE 
+    calculations.
diff --git a/docs/cite_us.md b/docs/cite_us.md
@@ -3,9 +3,9 @@ template: main.html
 title: Cite us
 ---
 
-**If you found gmx_MMPBSA useful for your research, please cite:**
-Coming soon!
+**If you found xBFreE useful for your research, please cite:**
 
+Coming soon!
 
 <a href="https://www.scimagojr.com/journalsearch.php?q=5100155074&amp;tip=sid&amp;exact=no" title="SCImago Journal 
 &amp; Country Rank"><img border="0" align="right" width=175 src="https://www.scimagojr.com/journal_img.php?id=5100155074" 
@@ -17,3 +17,5 @@ Valdés-Tresanco, M.S., Valdés-Tresanco, M.E., Valiente, P.A. and Moreno E. gmx
 End-State Free Energy Calculations with GROMACS. _Journal of Chemical Theory and Computation_, 2021 17 (10), 6281-6291. 
 [https://pubs.acs.org/doi/10.1021/acs.jctc.1c00645][1]. Download | [*.bib](gmx_MMPBSA_citation.bib)
 | [*.ris](gmx_MMPBSA_citation.ris)
+
+[1]: https://pubs.acs.org/doi/10.1021/acs.jctc.1c00645
diff --git a/docs/news/index.md b/docs/news/index.md
@@ -1,32 +1,3 @@
 # News
 
-
-```mermaid
-%%{
-  init: {
-    'theme': 'base',
-    'themeVariables': {
-      'primaryColor': '#BB2528',
-      'primaryTextColor': '#fff',
-      'primaryBorderColor': '#7C0000',
-      'lineColor': '#F8B229',
-      'secondaryColor': '#006100',
-      'tertiaryColor': '#fff'
-    }
-  }
-}%%
-        graph TD
-          A[Christmas] -->|Get money| B(Go shopping)
-          B --> C{Let me think}
-          B --> G[/Another/]
-          C ==>|One| D[Laptop]
-          C -->|Two| E[iPhone]
-          C -->|Three| F[fa:fa-car Car]
-          subgraph section
-            C
-            D
-            E
-            F
-            G
-          end
-```
+## Coming soon!
diff --git a/docs/project/people.md b/docs/project/people.md
@@ -10,59 +10,47 @@
 
         ![Image title](../assets/xbfree_logo.svg){ align=left width=250}
 
-    ### Mario S. Valdés Tresanco
+    ### [Mario S. Valdés Tresanco](https://www.researchgate.net/profile/Mario-Valdes-Tresanco-2)
     _PhD in Modeling and Scientific Computing_<br>
     Colombia    
 
     **Creator and Principal Developer**
 
-    Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nulla et euismod nulla. Curabitur feugiat, tortor non 
-    consequat finibus, justo purus auctor massa, nec semper lorem quam in massa.
-
 !!! info ""
 
     !!! info inline end ""
         
         ![Image title](../assets/xbfree_logo.svg){ align=left width=250}
 
-    ### Mario E. Valdés Tresanco
-    _PhD Student in Proteomic_ <br>
+    ### [Mario E. Valdés Tresanco](https://www.researchgate.net/profile/Mario-Valdes-Tresanco)
+    _PhD Student Biophysical-Chemistry_ <br>
     University of Calgary, Canada.
 
     **Creator and Principal Developer**
-
-    Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nulla et euismod nulla. Curabitur feugiat, tortor non 
-    consequat finibus, justo purus auctor massa, nec semper lorem quam in massa.
 
 !!! info ""
 
     !!! info inline end ""
 
         ![Image title](../assets/xbfree_logo.svg){ align=left width=250}
 
-    ### Pedro A. Valiente
-    _PhD_<br>
+    ### [Pedro A. Valiente](https://www.researchgate.net/profile/Pedro-Valiente)
+    _PhD in Biochemistry_<br>
     University of Toronto, Canada.
 
     **Academic Assessor**
 
-    Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nulla et euismod nulla. Curabitur feugiat, tortor non 
-    consequat finibus, justo purus auctor massa, nec semper lorem quam in massa.
-
 !!! info ""
 
     !!! info inline end ""
 
         ![Image title](../assets/xbfree_logo.svg){ align=left width=250}
 
-    ### Ernesto Moreno Frías
-    _PhD_<br>
+    ### [Ernesto Moreno Frías](https://www.researchgate.net/profile/Ernesto-Moreno-Frias)
+    _PhD in Biology_<br>
     University of Medellín, Colombia.
 
     **Academic Assessor**
 
-    Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nulla et euismod nulla. Curabitur feugiat, tortor non 
-    consequat finibus, justo purus auctor massa, nec semper lorem quam in massa.
-
 
 ## Contributors
diff --git a/docs/project/project.md b/docs/project/project.md
@@ -8,5 +8,6 @@ a project dedicated to implementing, testing, and developing BFE methods describ
 
 
 ## Motivation
-We believe that an idea, no matter how much potential it may have, dies in a scientific article if it cannot be 
-used in a simple and accessible way. 
+
+We strongly believe that even the most promising idea loses its potential if it remains confined to a scientific 
+article and cannot be utilized in a simple and accessible manner.
diff --git a/docs/project/roadmap.md b/docs/project/roadmap.md
@@ -1,13 +1,15 @@
 # Roadmap
-Our roadmap focuses on first implementing methods that are widely used. Initially, starting with gmx_MMPBSA, we 
-implemented most of the methods derived from PB. However, in the future, we want to implement several more methods, 
-like LIE, FEP, and TI.
+Our roadmap prioritizes the implementation of widely used methods. Currently, we have successfully implemented 
+gmx_MMPBSA, which incorporates several methods derived from PB and other implicit solvent-based approaches. 
+However, our future plans involve expanding our method offerings to include additional approaches such as 
+LIE, FEP, and TI.
 
 !!! important
-    It is important to clarify that our roadmap is tentative but does not guarantee that it is exact. As we mentioned, 
-    we do not have financing, so we can only dedicate our free time to the project development. If possible, 
-    consider [becoming a sponsor](../../sponsor#how-to-become-a-sponsor). Shortly, we plan to apply for financing that 
-    will allow full-time development and therefore have more exact release dates.   
+    Please note that our roadmap is subject to change and should be considered tentative. We cannot guarantee exact 
+    timelines as we currently lack financial resources and can only dedicate our free time to project development. 
+    However, we encourage you to consider becoming a sponsor to support our efforts. By becoming a sponsor, we can 
+    aim for full-time development and provide more accurate release dates in the future. For more information on 
+    sponsorship opportunities, please visit [becoming a sponsor](../../sponsor#how-to-become-a-sponsor).
 
 ```mermaid
 gantt