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Commit e0d1dbe7 authored by David W. Wright's avatar David W. Wright
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Add information on the template topology file provided and how to create a...

Add information on the template topology file provided and how to create a copy consistent with the later commands
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1 merge request!13Tutorial clarifications
...@@ -86,7 +86,8 @@ The output coordinates ``out.gro`` must be solvated using the GROMACS tool `gmx ...@@ -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 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. 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:: The three stages of simulation: minimisation, equilibration, and production may then be run::
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