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
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
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.
Potentials
Excel to XML Conversion
7.2.2. References¶
- 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).
- Martini v2.2 Force-Field Parameters, http://www.cgmartini.nl/images/parameters/ITP/martini_v2.2.itp