From e0d1dbe7d40253fd593e90d5a8c39ed2fe4401cd Mon Sep 17 00:00:00 2001
From: "David W. Wright" <dave.william.wright@gmail.com>
Date: Wed, 4 Jan 2017 11:50:58 +0000
Subject: [PATCH] Add information on the template topology file provided and
how to create a copy consistent with the later commands
---
doc/source/tutorial.rst | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/doc/source/tutorial.rst b/doc/source/tutorial.rst
index d3e9271..f5a0381 100644
--- a/doc/source/tutorial.rst
+++ b/doc/source/tutorial.rst
@@ -86,7 +86,8 @@ The output coordinates ``out.gro`` must be solvated using the GROMACS tool `gmx
gmx solvate -cp out.gro -cs ../../data/water.gro -o solv.gro -radius 0.21
Since MARTINI water cannot be automatically added to the `.top` file, this must be done manually.
-Add the line "W 251" to the bottom of the `.top` file, since 251 should be the number of water molecules added by `gmx solvate`.
+A template file, ``template.top``, is provided.
+Copy this to ``topol.top`` and add the line "W 251" to the bottom, since 251 should be the number of water molecules added by `gmx solvate`.
The three stages of simulation: minimisation, equilibration, and production may then be run::
--
GitLab