From 9f88329ebdf1302ab5c3332ab688e5888ad337c7 Mon Sep 17 00:00:00 2001 From: "David W. Wright" <dave.william.wright@gmail.com> Date: Wed, 4 Jan 2017 11:45:52 +0000 Subject: [PATCH] Edit the tutorial text to agree with the provided atomistic trajectory filenames --- doc/source/tutorial.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/source/tutorial.rst b/doc/source/tutorial.rst index af620ff..194e0c5 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. -- GitLab