From 577dfc6b415d0f1fe500b510e1f689a3aca148c3 Mon Sep 17 00:00:00 2001
From: James Graham <J.A.Graham@soton.ac.uk>
Date: Wed, 22 Mar 2017 15:14:01 +0000
Subject: [PATCH] Add note to readme and documentation about the importance of
 validation

---
 README.md            | 5 ++++-
 doc/source/index.rst | 4 ++++
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 925bb4e..ff69d2f 100644
--- a/README.md
+++ b/README.md
@@ -25,7 +25,7 @@ If you experience problems or wish to see a new feature added please [file an is
 If you find this useful, please cite as : `Graham, J. (2017). PyCGTOOL, https://doi.org/10.5281/zenodo.259330`
 
 ## Usage
-Input to PyCGTOOL is GROMACS GRO and XTC files, along with two custom files: MAP and BND.  These files provide the atomistic-to-CG mapping and bonded topology respectively.  Example files are present in the [test/data](https://github.com/jag1g13/pycgtool/tree/master/test/data) directory.  The format of these files is described in the [full documentation] (http://pycgtool.readthedocs.io/en/master/).
+Input to PyCGTOOL is GROMACS GRO and XTC files, along with two custom files: MAP and BND.  These files provide the atomistic-to-CG mapping and bonded topology respectively.  Example files are present in the [test/data](https://github.com/jag1g13/pycgtool/tree/master/test/data) directory.  The format of these files is described in the [full documentation](http://pycgtool.readthedocs.io/en/master/).
 
 To run PyCGTOOL:
 `pycgtool.py -g <GRO file> -x <XTC file> -m <MAP file> -b <BND file>`
@@ -36,6 +36,9 @@ To run PyCGTOOL in map-only mode:
 To see the help text:
 `pycgtool.py -h`
 
+For more information, see [the tutorial](https://pycgtool.readthedocs.io/en/master/tutorial.html).
+It is important to perform validation of any new parameter set; a brief example is present at the end of the tutorial.
+
 ## Requirements
 PyCGTOOL requires:
 * Python3
diff --git a/doc/source/index.rst b/doc/source/index.rst
index d3b584c..5eece82 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -62,6 +62,10 @@ Example mapping and bond definition files are present in the ``test/data`` direc
 
 After running PyCGTOOL two files, ``out.gro`` and ``out.itp`` will be created.  The gro file contains the mapped coarse-grain coordinates with every molecule for which a mapping was provided.  The itp file contains the parameters for each molecule type.
 
+It is important to perform validation of any new parameter set.
+This is typically done by comparing properties between the reference simulation and simulations using the new CG model.
+In the tutorial we use the radius of gyration, but there are many other suitable properties, depending on the class of molecule being parametrised.
+
 Mapping / Bond Definition Files
 -------------------------------
 The mapping and bond definition input files use a format similar to the GROMACS itp/top format.
-- 
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