I am trying to learn the cgdna package and use the python tool mentioned in page 5 of the following articlechrome-extension://efaidnbmnnnibpcajpcglclefindmkaj/https://docs.lammps.org/PDF/CG-DNA.pdf
And I put the quote here: To simplify the setup procedure we provide a simple
python tool with the example and utility files of the
USER-CGDNA package. The script allows the user to create
single- and double-stranded DNA from an input file
that specifies the sequence and requires an installation of
numpy.
The syntax is very straightforward, but the system size
has to be specified in the following way:
$> python generate.py
The output is written directly into a data file in LAMMPS
format. This has to be given in the LAMMPS input file.
is an ASCII input file that contains
keywords and the sequence of one ssDNA strand.
I have many problems with these words. How do I activate this tool they mentioned? Do I need to install anything? Or is this just their own tool that they kept to themselves? (I have the windows excecutable installed) Where do I type the command they offered?
Thank you for taking your time to read my question and if you can help me thanks even more.
You may want to contact the CG-DNA author directly. I don’t recall him responding to questions here. Contact info is here
They are bundled with the CG-DNA examples in the “examples/PACKAGES/cgdna” folder and below. If you cannot find them in your LAMMPS installation, you can download them from the GitHub repo here: lammps/examples/PACKAGES/cgdna at develop · lammps/lammps · GitHub
As can be inferred from the example you quoted, you need to have python installed.
You may run into Windows specific issues. Most LAMMPS users and specifically most LAMMPS developers us Linux (as it is the most common platform on HPC clusters and supercomputers) and thus test their tools often only on Linux.