diff --git a/README.md b/README.md index 925bb4ef52ed9e61024c7ff073b30e98f7dcaea7..ff69d2ff75f8fc2f0b1b01439358e371c0160075 100644 --- a/README.md +++ b/README.md @@ -25,7 +25,7 @@ If you experience problems or wish to see a new feature added please [file an is If you find this useful, please cite as : `Graham, J. (2017). PyCGTOOL, https://doi.org/10.5281/zenodo.259330` ## Usage -Input to PyCGTOOL is GROMACS GRO and XTC files, along with two custom files: MAP and BND. These files provide the atomistic-to-CG mapping and bonded topology respectively. Example files are present in the [test/data](https://github.com/jag1g13/pycgtool/tree/master/test/data) directory. The format of these files is described in the [full documentation] (http://pycgtool.readthedocs.io/en/master/). +Input to PyCGTOOL is GROMACS GRO and XTC files, along with two custom files: MAP and BND. These files provide the atomistic-to-CG mapping and bonded topology respectively. Example files are present in the [test/data](https://github.com/jag1g13/pycgtool/tree/master/test/data) directory. The format of these files is described in the [full documentation](http://pycgtool.readthedocs.io/en/master/). To run PyCGTOOL: `pycgtool.py -g <GRO file> -x <XTC file> -m <MAP file> -b <BND file>` @@ -36,6 +36,9 @@ To run PyCGTOOL in map-only mode: To see the help text: `pycgtool.py -h` +For more information, see [the tutorial](https://pycgtool.readthedocs.io/en/master/tutorial.html). +It is important to perform validation of any new parameter set; a brief example is present at the end of the tutorial. + ## Requirements PyCGTOOL requires: * Python3 diff --git a/doc/source/index.rst b/doc/source/index.rst index d3b584c5f7f0d6b70dc869ac0053b4cbd46a23dc..5eece8247998a46ce947946c391db543eecfe9bd 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -62,6 +62,10 @@ Example mapping and bond definition files are present in the ``test/data`` direc After running PyCGTOOL two files, ``out.gro`` and ``out.itp`` will be created. The gro file contains the mapped coarse-grain coordinates with every molecule for which a mapping was provided. The itp file contains the parameters for each molecule type. +It is important to perform validation of any new parameter set. +This is typically done by comparing properties between the reference simulation and simulations using the new CG model. +In the tutorial we use the radius of gyration, but there are many other suitable properties, depending on the class of molecule being parametrised. + Mapping / Bond Definition Files ------------------------------- The mapping and bond definition input files use a format similar to the GROMACS itp/top format.