7.2. Data Curation for Coarse-Grained Force-Field Data

7.2.1. The Martini Coarse-Grained Force-Field

In this tutorial, we show step by step how to curate data for the Martini Coarse-Grained Force-Field into WebFF using the WebFF Excel data template and the WebFF.py Python library.

Martini Force-Field Data Source
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WebFF Excel Spreadsheet Data Entry

The data for the Martini force-field was ported to the Excel spreadsheet called: WebFF-DocumentationXMLCoarse-GrainedWebFF-CoarseGrained-DataTemplate.xlsx

Metadata

There are three sections of Metadata to include

_images/CG_template_Metadata.png
_images/CG_template_Keywords.png
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Atom Types

The atom types for Martini are general in nature, and each entry can stand for a number of similar but related chemical moeities.

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Potentials
_images/CG_template_Bonds.png
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Excel to XML Conversion
_images/Python_cmd_line_Excel_to_XML.png

7.2.2. References

  1. Siewert J. Marrink, H. Jelger Risselada, Serge Yefimov, D. Peter Tieleman, and Alex H. de Vries, “The MARTINI Force Field:  Coarse Grained Model for Biomolecular Simulations,” J. Phys. Chem. B, 111 (27), pp 7812–7824, (2007).
  2. Martini v2.2 Force-Field Parameters, http://www.cgmartini.nl/images/parameters/ITP/martini_v2.2.itp