GROMACS: periodic molecules (bonded across the cell boundary), and a first-run walkthrough
还没有人认领这个 Issue。
评估
- 难度
- 4/5
- 预计耗时
- 3-5 天
- 新手友好度
- 30/100
- Issue 类型
- 功能
- 描述清晰度
- 基本清楚
- 活跃度
- 活跃
调研方向
Start with the GROMACS editors, where the periodic-molecules setting would be added, and with the .mdp that ECCE writes, which currently has no such line. The payload names no source files. Check qe-first-calculation for the walkthrough format. Done means the setting appears in the editors and in the written .mdp, and the walkthrough steps match hand-run gmx output. Related: #253, #260.
由索引模型根据 Issue 内容生成。
描述
1. periodic-molecules. The .mdp ECCE generates has no periodic-molecules setting, and the editors offer none. Infinite periodic systems (clays, other minerals, MOFs, crystals; the MINFF clay set uses periodic-molecules = yes) have bonds through the periodic boundary, so they need it, or mdrun fails or computes them wrongly. Add it to the GROMACS editors (on by default when the topology has bonds longer than half a box vector, or when the structure is marked periodic), and write it into the .mdp.
2. Help: a GROMACS walkthrough, like qe-first-calculation: a small system (a water box or a small solvated molecule) through minimisation → NVT → NPT → MD in ECCE. It should cover:
- which files are attached where (structure, topology, include files / force-field folder, #260);
- what each stage does;
- how to read the results (energies, structure, trajectory).
Each step is checked against running gmx by hand. A user who has never used GROMACS currently has no way in.
Related: #253, #260.
- 主要语言
- C
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- 10
- 派生
- 8
- 平均合并
- 21 分钟
- 30 天内合并 PR
- 1
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