Quick Start

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 that 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 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.

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.