From 8b4fdc9ebbd587e8529047b2debd5e6cc31cbbd8 Mon Sep 17 00:00:00 2001
From: luciannahss <luciannahss@gmail.com>
Date: Mon, 30 Sep 2024 13:17:22 -0300
Subject: [PATCH] Update NAMD tutorial 1

---
 docs/source/Developers.rst      |  2 ++
 docs/source/NAMD/Tutorial-1.rst | 15 ++++++++++++++-
 2 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/docs/source/Developers.rst b/docs/source/Developers.rst
index ed01929..2601714 100644
--- 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
index 92b54e1..7182b3f 100644
--- 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