Resolution transformation

Backward

 

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

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.

Resolution transformation

 

Custom version of Gromacs to reintroduce atomistic details to CG structures gmx_rev.tar.gz

If you use the code, please cite:

We recommend you use Backward instead of this tool. For details about this tool please contact Andrzej Rzepiela (This email address is being protected from spambots. You need JavaScript enabled to view it.)

You may also try an automized resolution transformation provided by Angel Pineiro, see http://smmb.usc.es/sugarpie/sugarpie.php