From e35ae3fb70a8b5fc93794a155867f3fa4178be54 Mon Sep 17 00:00:00 2001
From: MaciejMajew <maciej.k.majewski@gmail.com>
Date: Wed, 21 Jun 2023 11:17:26 +0200
Subject: [PATCH] supplement for the description

---
 README.md                                  | 2 +-
 Tutorials/1-Tutorial-CG-NNP-Training.ipynb | 8 +++++++-
 Tutorials/2-Tutorial-CG-Simulation.ipynb   | 5 +++++
 3 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index ecbf4a7..630dcc2 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 # Machine Learning Coarse-Grained Potentials of Protein Thermodynamics
 
-This repository contains code, data and tutarial for reproducing the paper "Machine Learning Coarse-Grained Potentials of Protein Thermodynamics". 
+This repository contains code, data and tutarial for reproducing the paper "Machine Learning Coarse-Grained Potentials of Protein Thermodynamics". https://arxiv.org/abs/2212.07492
 
 ## Background
 
diff --git a/Tutorials/1-Tutorial-CG-NNP-Training.ipynb b/Tutorials/1-Tutorial-CG-NNP-Training.ipynb
index 16acba1..935370d 100644
--- a/Tutorials/1-Tutorial-CG-NNP-Training.ipynb
+++ b/Tutorials/1-Tutorial-CG-NNP-Training.ipynb
@@ -1,6 +1,7 @@
 {
  "cells": [
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -15,6 +16,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -33,6 +35,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -52,6 +55,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -102,6 +106,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -109,6 +114,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -203,7 +209,7 @@
     "```\n",
     "where `$PATH` is the path to your `torchmd-net` repo.\n",
     "\n",
-    "The training saves 8 best epochs. The progress of the training is saved in TensorBoard session. The training and validation curves for the training of full Chignolin dataset are presented here:"
+    "The training saves 8 best epochs. The progress of the training is saved in TensorBoard session. The training requires a GPU and should take a couple of hours on a standard GPU."
    ]
   }
  ],
diff --git a/Tutorials/2-Tutorial-CG-Simulation.ipynb b/Tutorials/2-Tutorial-CG-Simulation.ipynb
index 6dabbbb..ecd2839 100644
--- a/Tutorials/2-Tutorial-CG-Simulation.ipynb
+++ b/Tutorials/2-Tutorial-CG-Simulation.ipynb
@@ -1,6 +1,7 @@
 {
  "cells": [
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -24,6 +25,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -31,6 +33,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -83,6 +86,8 @@
     "\n",
     "where `$PATH` is a path to your `torchmd` repo (not `torchmd-net` linke in `1-Tutorial-CG-NNP-Training.ipynb`)\n",
     "\n",
+    "The simulation GPU and should take a couple of hours on a standard GPU, however can be also run on a CPU.\n",
+    "\n",
     "Now we will go through options in a configuration file:\n",
     "\n",
     "* First we define `device`, the directory `log_dir` and name of the output files `output`.\n",