polyply 0.0.1

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polyply

Functionality

Polyply is a python suite designed to facilitate the generation of input files for simulating bio-macromolecules with GROMACS. It is possible to generate both itp and coordinates files for most (bio) macromolecules such as synthetic polymers or polysaccharides. It also facilitates manipulation of itp files and structures to extend or change already existing files. A library for some commonly used macro molecules using different force-fields (martini, gromos) is included. In principle the program can be used with any type of force-field (FF).

Make sure to always verify the results and give appropriate credit to the developers of the force-field, molecule parameters and this program.

Installation

Polyply requires python 3.6 or greater. It is distributed via PyPi, and can be installed using the pip command:

pip install polyply

This installs the last released version. You can update an existing installation by running pip install -U polyply. In some cases you may want to experiment with running the latest development version. You can install this version with the following command:

pip install git+https://github.com/fgrunewald/polyply_1.0.git#polyply_1.0

The behavior of the pip command can vary depending of the specificity of your python installation. See the documentation on installing a python package to learn more.

Polymer Library

Some macro molecules are implemented in our library for a range of different force-fields. To get a list of all libraries available run:

polyply -list-lib

To get a detailed list of all the individual macro molecules:

polyply -list-blocks <Force Field Name>

Note that while you can combine fragments from different libraries (e.g. the martini-3 polymer library with martini-3 proteins), we cannot guarantee that all the links are present to make a meaningful itp. All blocks within a library can safely be combined. For more information on how to implement links between different blocks see the wiki.

Itp file generation

To generate a linear polymer chain using parameters, provided in the library run:

polyply gen_itp -lib <library_name> -name <name> -seq <monomer:#number> -o <name_outfile + .itp>

For more information on how to generate itp-files for more complex polymers or how to combine them with existing itp-files see the wiki pages.

Initial structure generation

To generate an initial structure run:

polyply gen_coords -p <top> -o <name_outfile + .gro> -name <name of molecule> -dens <density>

or:

polyply gen_coords -p <top> -o <name_outfile + .gro> -name <name of molecule> -box <x, y, z>

In order to append coordinates to an already existing coordinate file run:

polyply gen_coords -p <top> -o <name_outfile + .gro> -name <name of molecule> -c <init_coords.gro> -box <x, y, z>

or

polyply gen_coords -p <top> -o <name_outfile + .gro> -name <name of molecule> -c <init_coords.gro> -dens <density>

Note that at the moment polyply can only generate disordered structures of polymers. All molecules that have secondary structure (e.g. DNA, proteins) cannot be generated accurately. At the moment chirality is also not taken into account. All polymers are atactic unless a dihedral specifies the chirality.

Contributions

The development of polyply is done on github. Contributions are welcome as bug reports and pull requests. Note however that the decision of whether or not contributions can give authorship on the resulting academic paper is left to our sole discretion.

License

Polyply is distributed under the Apache 2.0 license.

Copyright 2020 University of Groningen

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

	http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

The full text of the license is available in the source repository.