Concatenate molecular dynamics trajectories into a combined DCD and reference PDB.
npx skills add https://github.com/matsunagalab/mdclaw --skill md-analyze
Please help me install this Agent Skill. Skill: MD Analyze Source: https://github.com/matsunagalab/mdclaw/tree/main/skills/md-analyze Command: npx skills add https://github.com/matsunagalab/mdclaw --skill md-analyze
Automatically consolidates fragmented MD trajectories from a prod lineage into a single, memory-efficient combined trajectory and provides a reference structure for downstream analysis.
Run the MD Analyze workflow to concatenate the prod trajectory lineage into a single combined trajectory and generate a reference structure for downstream analyses.
High-intent search queries and answers about installing and using this skill.
To concatenate molecular dynamics trajectories, you can stream and combine fragmented prod trajectory frames into a single memory-efficient combined trajectory. This process uses parameters like --selection, --stride, and --chunk to manage atom subsets and frame streaming.
Preparing a reference structure for RMSD and RMSF analysis involves generating a reference_pdb file alongside your combined trajectory. The workflow outputs this reference structure and selection_indices to provide the necessary baseline for cross-tool structural comparisons.
Yes, you can analyze large MD trajectories in chunks to avoid memory limits by using a streaming concatenation approach. The workflow supports a --chunk parameter to stream frames efficiently, producing a compact combined trajectory without loading everything into memory at once.
The best way to select specific atoms when combining MD simulation trajectories is to use the --selection parameter during the streaming concatenation workflow. This generates a combined trajectory containing only your chosen atom subsets and outputs the corresponding selection_indices.
Metadata generated for downstream molecular dynamics distance analyses includes n_atoms_selected, total_frames, frames_per_source, source_trajectories, and prmtop_file. This node metadata ensures reproducible analyses when calculating distances across consolidated trajectory artifacts.
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