Welcome to PySoftK’s documentation!
Python Soft-matter King’s College London (PySoftK) is a set of tools and Python modules for setting up, manipulating, and running atomistic simulations of polymers. The code is freely available under the GNU General Public License v3.0.
PySoftK provides interfaces to different codes through pysoftk.linear_polymer.calculators which are used together with
pysoftk.linear_polymer.super_monomer for creating and running atomistic molecular dynamics simulations for a broad range of polymeric materials.
By simply inputting the SMILES code(s) for the desired monomer(s), the code allows the user to build polymers with different compositions (homopolymers, block heterpolymers, sequenced heteropolymers and random heteropolymers) and topologies (linear and ring). In the end the code generates an equilibrated structure of the polymer that can be used as an input for building the desired initial configuration for a molecular dynamics simulation.
Contents:
- About
- Usage
- Tutorials: Modelling Polymers
- Preparing monomers for PySoftK
- From single molecules to polymers using PySoftK
- Creating a Polymer
- Creating chains of Polymers
- Creating diblock Polymers
- Creating random Polymers
- Creating cyclic Polymers
- Creating branched Polymers
- Creating patterned Polymers
- Modelling soft-matter long chain polymers
- Creating new polymers from different modules
- Automatic Folder Creation
- Computing using ab-initio calculators
- Automatic torsional angle detection for planar polymers
- Tutorials: Analysis Tools
- Tutorial on the usage of contacts
- Tutorial on the usage of ecc_micelle
- Tutorial on the usage of intrinsic_density_micelle tool
- Tutorial on the usage of micelle_whole tool
- Tutorial on the usage of rgyr_micelle
- Case example of MDAnalysis vs Pysoftk’s rgyr_micelle
- Tutorial on the usage of RSA tool
- Tutorial on the usage of RSA tool
- Tutorial on the usage of SCP tool
- Tutorial on the usage of hydration
- Tutorial on the usage of spherical_density tool
- Frequently Asked Questions
- pysoftk