diff --git a/doc/source/pycgtool.pycgtool.rst b/doc/source/pycgtool.pycgtool.rst new file mode 100644 index 0000000000000000000000000000000000000000..1b881834dd96f97892376a847ad061526a61945f --- /dev/null +++ b/doc/source/pycgtool.pycgtool.rst @@ -0,0 +1,7 @@ +pycgtool.pycgtool module +======================== + +.. automodule:: pycgtool.pycgtool + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/tutorial.rst b/doc/source/tutorial.rst new file mode 100644 index 0000000000000000000000000000000000000000..d03c1cd3143276d8cf79777b0c83b1c258c4172f --- /dev/null +++ b/doc/source/tutorial.rst @@ -0,0 +1,41 @@ +PyCGTOOL Tutorial +================= + +This tutorial follows the complete process of parametrising a new molecule within the MARTINI forcefield, covering aspects of mapping design, model generation and model validation. +PyCGTOOL is used at multiple stages, showing its use in several different situations. + +The molecule chosen as a target for this parametrisation is the :math:`\beta_1` antagonist atenolol. + + +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. +Currently, PyCGTOOL is limited to trajectories in the GROMACS XTC format, with a single frame GRO for residue information. + +Mapping Design +-------------- +Designing a suitable mapping from the atomistic to the coarse-grained representation requires some experience and a degree of `chemical intuition`, but the ease with which the mapping may be modified using PyCGTOOL allows the mapping to be iterated much more quickly. + +The process of designing a mapping involves splitting the molecule into fragments, each of which contains approximately four heavy atoms. +Start by finding functional groups such as amides or carboxylates, each of which may become a single bead. +Next, replace phenyl rings with a triangle of three `small` type beads, each of which contains two heavy atoms and has reduced Lennard-Jones size and mass, as compared to the normal four-atom beads. +Finally, divide any remaining parts of the molecule into beads of four heavy atoms as required. +The ideal bead will contain four heavy atoms and be nearly spherical, but this is not always possible. +If any atoms remain after clusters of four have been allocated, it may be required to use a mapping of three-to-one for some beads. + +After the atoms have been allocated to beads, determine which beads should be bonded by copying the bonds between their component atoms. +It will probably be the case that there is no obviously best mapping and bond topology, which is not at this point a major issue as multiple mappings can be assessed easily. + +Once the mapping and bond topology have been determined, they must be put into a format readable by PyCGTOOL. +This format is as described in the introduction to PyCGTOOL. + +Model Generation +---------------- + +Running the CG Simulation +------------------------- + +Model Validation +---------------- +