Merge pull request #79 from luciannahss/lu-sirah-doc

Update NAMD tutorial 1
SIRAHFF · Sep 30, 2024 · 7582b14 · 7582b14
2 parents 4738b0e + 8b4fdc9
commit 7582b14
Show file tree

Hide file tree

Showing 2 changed files with 16 additions and 1 deletion.
diff --git a/docs/source/Developers.rst b/docs/source/Developers.rst
@@ -12,6 +12,8 @@ Developers
 
 *    Andres Ballesteros
 
+*    Antonella Alba
+
 *    Ezequiel N. Frigini  
 
 *    Matias Machado  

diff --git a/docs/source/NAMD/Tutorial-1.rst b/docs/source/NAMD/Tutorial-1.rst
@@ -3,7 +3,7 @@
    Please report bugs, errors or enhancement requests through `Issue Tracker <https://github.com/SIRAHFF/documentation/issues>`_ or if you have a question about SIRAH open a `New Discussion <https://github.com/SIRAHFF/documentation/discussions>`_.
 
 This tutorial shows how to use the SIRAH force field to perform a coarse grained (CG) simulation of a protein in explicit solvent (called WatFour, WT4). The main references for
-this tutorial are: `Darré et al. <https://pubs.acs.org/doi/abs/10.1021/ct100379f>`_, `Machado et al. <https://doi.org/10.1021/acs.jctc.9b00006>`__ and `Machado & Pantano  <https://academic.oup.com/bioinformatics/article/32/10/1568/1743152>`_. We strongly advise you to read these articles before starting the tutorial.
+this tutorial are: `Cantero et al. <https://doi.org/10.1021/acs.jpcb.4c03278>`_, `Darré et al. <https://pubs.acs.org/doi/abs/10.1021/ct100379f>`_, `Machado et al. <https://doi.org/10.1021/acs.jctc.9b00006>`__ and `Machado & Pantano  <https://academic.oup.com/bioinformatics/article/32/10/1568/1743152>`_. We strongly advise you to read these articles before starting the tutorial.
 
 .. important::
 
@@ -274,6 +274,12 @@ The folder ``sirah.amber/tutorial/NAMD/1/NAMD2`` contains typical input files fo
 
     In this stage, the restriction file ``prot_restraints.pdb`` is assigned to the consref and conskfile flags.
 
+**Solvent equilibration (NPT):**
+
+.. code-block:: bash
+
+    namd2 +p8 eq1.conf > eq1.log &
+	
 **Soft equilibration to improve side chain solvation (NPT):**
 
 .. code-block:: bash
@@ -372,6 +378,13 @@ The folder ``sirah.amber/tutorial/NAMD/1/NAMD3`` contains typical input files fo
 
     In this stage, the restriction file ``prot_restraints.pdb`` is assigned to the consref and conskfile flags.
 
+**Solvent equilibration (NPT):**
+
+.. code-block:: bash
+
+    namd3 +p4 eq1.conf > eq1.log &
+
+
 **Soft equilibration to improve side chain solvation (NPT):**
 
 .. code-block:: bash