Resolution transformation

TS2CG: Triangulated Surfaces to Coarse Grain

Details: Last Updated: Friday, 03 April 2020 15:43

TS2CG is an algorithm to backmap a triangulated surface to a corresponding coarse-grained model.

The software can be downloaded from this link, or by visiting https://github.com/marrink-lab/TS2CG.

Backward

Details: Last Updated: Sunday, 20 August 2017 09:22

Backward is a tool to convert a coarse-grained system to united-atom or all-atom resolution. The mapping is done using a library of mapping definitions, which encode the geometric reconstruction.

In most cases, the backmapping is performed using the wrapper initram.sh, which calls backward.py and subsequently relaxes the resulting structure through energy minimization and molecular dynamics based relaxation.

When using this method, please cite:

Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models
Tsjerk A. Wassenaar, Kristyna Pluhackova, Rainer A. Böckmann, Siewert J. Marrink, and D. Peter Tieleman
J. Chem. Theory Comput., 10:676-690, 2014.
DOI: 10.1021/ct400617g

More extensive information and a tutorial can be found on the Martini website, follow this link.

The scripts and mapping definitions for gromacs versions 4 and 5-bead oleoyl lipid chains are combined into a single zip file, which can be downloaded here.

The initram.sh script for version 5 can be downloaded here.

When your system has lipids, we recommend downloading the mapping files for them from the lipidome library.

The script for gromacs versions 5 and higher and the mapping files for the amino acid residues and nucleobases are combined into a single zip file, which can be downloaded here.

Convert Martini water to polarizable water

Details: Last Updated: Thursday, 17 August 2017 15:13

triple-w.py

Script to convert the water in CG Martini system to polarizable water. For an example how to use this script, click here.