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GROMACS: MINFF mineral force field (structure → atom types/charges → MD)

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評価

難易度
5/5
見積もり時間
1週間以上
初心者へのやさしさ
25/100
issue の種類
機能追加
明瞭さ
おおむね明確
活発さ
活発
技術スタック
python
領域
backend, databases

調査の方向性

Start by reviewing the existing GROMACS MD workflow in issue #106 and the MINFF/atomipy assignment workflow described here. The issue names no ECCE implementation files or tests; its proposed tests use kaolinite and montmorillonite from minff's Systems folder and compare against atomipy output, then run grompp and a short energy minimisation. Done means the full structure-to-assignment-to-simulation workflow works in ECCE, including reported charges and untyped atoms.

索引モデルが issue の本文から書いたものです。

説明

Goal

Support the MINFF force field for minerals in ECCE's GROMACS workflow: clay minerals, oxides, hydroxides and zeolites, with Si, Al, Fe, Mg, Ca, Ti, Li and F. A user should be able to take a mineral unit cell, build a simulation cell from it, have MINFF atom types and charges assigned, and run energy minimisation, equilibration and dynamics, all from ECCE.

This builds on GROMACS activation via the MD workflow (#106, in progress on wip/gromacs-md).

What MINFF consists of

  • Parameters as a GROMACS force-field directory (min.ff):

    • a general set (GMINFF) and mineral-specific sets (TMINFF, over 30 minerals);
    • each set in four angle force constants (0, 250, 500 and 1500 kJ/mol/rad²);
    • oxygen Lennard-Jones parameters taken from the OPC3 water model by default.

  • Atom-type and charge assignment, which is structure-dependent:

    • types come from nearest neighbours;
    • oxygen charges are computed per system (charge smearing after Lammers et al. 2017), e.g. around isomorphic substitutions and edge groups.

    This is implemented in atomipy (Python, PyPI, MIT licence) and in the MATLAB/Octave atom library. ECCE therefore has to run the assignment rather than only ship parameter files.

  • Example systems (unit cells, conf.mdp, topol.top) in the minff repository.

Proposed workflow in ECCE

  1. Structure:
    • import a mineral unit cell (.pdb, .gro, CIF), with the cell vectors;
    • replicate it to a supercell (n_a × n_b × n_c);
    • optionally substitute atoms with a minimum separation (e.g. Al→Mg), as atomipy does.
  2. Force-field choice:
    • general or mineral-specific MINFF (mineral list taken from min.ff);
    • angle force constant;
    • water model.
  3. Assignment:
    • ECCE runs atomipy;
    • it writes the mineral .itp, the .gro and a topol.top that includes min.ff;
    • it reports the total charge and any atoms left untyped.
  4. Show the result:
    • atoms coloured by MINFF type;
    • charges available as a property.
  5. Simulation with the GROMACS MD tasks (#106): EM → NVT/NPT → MD, with .mdp presets derived from the minff example conf.mdp.
  6. Later:
    • solvation and counter-ions (hydrated clays, e.g. Na-montmorillonite);
    • analysis (#180).

Design rules

  • The topology builder is a wx-free component with a command-line entry point and tests. The ECCE windows only collect the choices and display results.
  • Tests: kaolinite and montmorillonite from the minff Systems folder are built with ECCE's builder. They are checked against topologies produced by atomipy run directly (atom types, charges, total charge), and then go through grompp and a short EM with real GROMACS.
  • Parameter files: min.ff is fetched from the minff repository at build/test time and not copied into this repository. It can be bundled once the minff repository carries a licence.
  • Platforms: Linux and macOS (Homebrew gromacs).

Open questions for GROMACS/MINFF users

  • Which minerals and systems should come first?
  • Is the general set with k = 500 the right default?
  • Should ECCE offer CLAYFF (also supported by atomipy) alongside MINFF?
  • Which .mdp settings should the presets use: cut-offs, PME, thermostat/barostat, semi-isotropic pressure coupling for clay layers?
主要言語
C
スター
10
フォーク
8
平均マージ
21分
マージ済み PR（30日）
1

環境構築

このプロジェクトには開発コンテナ、Dockerfile、コントリビューションガイドがありません。まず README を読み、一般的な手順ははじめてのコントリビューションガイドを参照してください。

はじめの一歩

  1. issue を最後まで読み、次にプロジェクトのコントリビューションガイドを読みます。
  2. 着手することを issue にコメントします — 二人が同じ作業をするのを防げます。
  3. リポジトリをフォークし、ブランチを切って変更します。
  4. issue 番号を参照したプルリクエストを送ります。

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