diff --git a/doc/source/tutorial.rst b/doc/source/tutorial.rst index af620fff391d19179450c6cc0e5e4e05a10e9321..194e0c5421e7f7c6e3e2afbaa5bc4093fa00e3a0 100644 --- a/doc/source/tutorial.rst +++ b/doc/source/tutorial.rst @@ -12,7 +12,7 @@ Atomistic Simulation -------------------- The reference simulation for the parametrisation of atenolol was performed using the GROMOS 54A7 united atom forcefield with a topology from the `ATB database <https://atb.uq.edu.au/molecule.py?molid=23433>`_. A single molecule of atenolol was solvated and equilibrated, before collecting a 50 ns trajectory using the GROMACS molecular dynamics simulator. -A reduced copy of this trajectory is provided in the tutorial files since the original is prohibitively large. +A reduced copy of this trajectory is provided in the tutorial files (as ref.xtc, ref.gro contains the initial structure) since the original is prohibitively large. Mapping Design -------------- @@ -72,7 +72,7 @@ Model Generation The process of model generation after having created the mapping and bond definition files is automated by PyCGTOOL. In the simplest case, a parameter set may be generated simply by passing the four input files to PyCGTOOL:: - pycgtool.py -g atenolol.gro -x atenolol.xtc -m atenolol.map -b atenolol.bnd + pycgtool.py -g ref.gro -x ref.xtc -m atenolol.map -b atenolol.bnd This will create two output files ``out.gro``, the mapped CG coordinates, and ``out.itp``, the calculated CG model parameters.