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Quick Start

This page gives an overview of the most important commands. For in-depth examples, see the Tutorials.

Polymer library

Some macromolecules 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 macromolecules:

polyply -list-blocks <Force Field Name>

Note

While you can combine fragments from different libraries (e.g. the martini3 polymer library with martini3 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 Writing .ff Input Files.

See the Polymer Library page for the full catalogue of currently available parameters.

itp file generation

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

polyply gen_params -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 Tutorials and the Syntax Reference.

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

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. Chirality is also not taken into account by default; all polymers are atactic unless a dihedral specifies the chirality.