From 7f8fd496761623a25ebf9ff0bfbd545be4b98ec1 Mon Sep 17 00:00:00 2001 From: Chi Cheng Date: Tue, 21 Jan 2025 17:18:06 +0000 Subject: [PATCH] small edits to tutorial 1 --- tutorials/tutorial1-phase-transition/README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/tutorials/tutorial1-phase-transition/README.md b/tutorials/tutorial1-phase-transition/README.md index 8a8abd9..bed2b0c 100644 --- a/tutorials/tutorial1-phase-transition/README.md +++ b/tutorials/tutorial1-phase-transition/README.md @@ -1,4 +1,4 @@ -# MDANSE Tutorial: a phase transition +# MDANSE Tutorial 1: a phase transition This tutorial will show you: * how to convert a LAMMPS trajectory to the MDANSE format, @@ -82,7 +82,7 @@ create plain text output of analysis. Please read: # The actual tutorial, step by step. -In the text of the tutorial, we will be concentrate on the +In the text of the tutorial, we will concentrate on the MDANSE GUI. However, the conversion and analysis jobs can be run also without the GUI. The scripts for running all the parts of the tutorial are provided in `md_inputs/script*`. @@ -162,7 +162,7 @@ the 'bonds' option of the visualiser. Press the play button to start the animation. (If you don't have the patience to watch every single frame, you can press fast forward instead.) -**Question**: What is the difference between the structures +**Question 1**: What is the difference between the structures in the beginning and at the end of the simulation? ## Calculate the temperature of the system @@ -215,7 +215,7 @@ The temperature values in the log file were calculated by the MD engine based on the velocity values at those specific simulation steps. -**Question**: The MDANSE temperature values don't match +**Question 2**: The MDANSE temperature values don't match the values in the log. Why? ## Calculate the Root Mean Square Displacement of atoms @@ -241,7 +241,7 @@ root mean square displacement of atoms from the reference position (which in our analysis was the initial position). -**Question**: Based on this plot, the system has +**Question 3**: Based on this plot, the system has melted in the second half of the simulation. At what temperature did the melting occur?