diff --git a/doc/source/tutorial.rst b/doc/source/tutorial.rst index d3e9271aa2597d88b8e1b4d5122bf1d566b29521..f5a0381341ec7404afbb09ec9c22d4ac64c5a273 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::