Bacterial cell wall peptidoglycan

A Martini model of bacterial cell wall peptidoglycan is now available, thanks to the nice work of Vaiwala et al. Download the files here!
Any queries regarding the model should be addressed to the authors (see below). 
The zip-archive contains the forcefield parameters (.itp) files and the structure (.gro) files of the single, 7, and 21 chains conformer for the peptidoglycan layer of the bacterial cell envelope, along with the README file. The details for the parameterization can be found in:
Rakesh Vaiwala, Pradyumn Sharma, Mrinalini Puranik, K. Ganapathy Ayappa. Developing a Coarse-Grained Model for Bacterial Cell Walls: Evaluating Mechanical Properties and Free Energy Barriers, J. Chem. Theory Comput. 2020, 16, 8, 5369–5384

Collagen Triple Helix

Collagen triple helix in vacuum

(provided by Markus Buehler)

Note: the required 'collagen.itp' file can be generated using the martinize script

Actin with ADP and ATP

Interested in using Martini for ADP or ATP with actin?

The attached .zip -file contains topologies for ADP, ATP as well as ADP-actin and ATP-actin systems. PDB files are provided for ADP- and ATP-actin, as well as the F-actin strand. As an added bonus, there's a short bash script which allows the user to build fibers of arbitrary lengths from one of the PDB files (2zwh.pdb).


Download the files here!

Toy peptide

The toy peptide contains all amino acids.
Half of the peptide is helical, the other half beta strand.
Equilibrated at T=300K, P=1 bar.
System composition: 1 peptide, water 1538.


Amyloid Fibrils

(provided by Jesper Sorensen)

Equilibrated at T=300K, constant pressure P=1 bar.
System size: 27 hiAPP (human islet amyloid polypeptide) fibrils,  59271 waters