quickMD-nf

A Nextflow pipeline to perform molecular dynamics (MD) simulations and analysis of proteins in solution.

Overview

[One or two paragraphs: what the pipeline simulates, the MD engine used (e.g. GROMACS/OpenMM), and what analyses it outputs.]

Requirements

• Nextflow (>= 23.x)
• A container runtime: Docker or Singularity (see containers/)
• [MD engine + any Python/analysis dependencies]

Repository structure

quickMD-nf/ ├── .github/workflows/ # CI build workflows ├── bin/ # Helper / analysis scripts ├── conf/ # Configuration profiles ├── containers/ # Container definitions (Docker/Singularity) ├── testdata/ # Small test dataset ├── main.nf # Pipeline entry point ├── nextflow.config # Default configuration ├── proton_list*.txt # Protonation input lists (see below) └── readme.md

Results

Each run produces re-centred PDB structures from the OpenMM MD stage, organised by run date.

Directory layout

results_30ns_salting/
└── <YYYY-MM-DD>/                # run date
    └── openmm-md/               # OpenMM MD stage
        └── wildtype_center_box_<salt>_<pH>_<temp>_traj<N>.pdb

Note: early runs (March 2025) use a flattened form, results_30ns_salting_<YYYY-MM-DD>/openmm-md/…, where the date is appended with an underscore. From April 2025 onwards the date is a nested subdirectory. New runs should follow the nested convention.

File naming convention

wildtype_center_box_0.1500M_4.6pH_310K_traj1.pdb

Field	Example	Description
variant	wildtype	Protein variant
processing	center_box	Re-centred in the simulation box
salt	0.1500M	NaCl concentration (0.15 M)
pH	4.6pH	Protonation pH
temperature	310K	Temperature (310 K, 37 °C)
replicate	trajN	Independent trajectory number

Simulation matrix

All simulations: wildtype, 0.1500 M salt, 310 K, 30 ns.

pH	Replicates	Trajectories
4.6	3	traj1–3
4.8	3	traj1–3
5.0	3	traj1–3
5.2	3	traj1–3
5.4	3	traj1–3
5.6	3	traj1–3
5.8	3	traj1–3
6.0	3	traj1–3
6.2	3	traj1–3
6.4	3	traj1–3
6.6	3	traj1–3
6.8	3	traj1–3
7.0	3	traj1–3
7.2	3	traj1–3
7.4	18	traj1–18

Total: 15 pH conditions, 60 trajectory structures.

Protonation variant: deprotonated H225 (HIE)

A second series removes a single proton from the His225 (H225) side chain, modelling it as the neutral HIE tautomer (proton retained on the epsilon nitrogen, NE2). This corresponds to the intrajH225HIE set in the analysis scripts. These runs share the base conditions of the titration set — wildtype, 0.1500 M salt, pH 4.6, 310 K, 30 ns — with an added removed_protons_<...> token in the file name.

File naming convention

wildtype_center_box_0.1500M_4.6pH_removed_protons_194_155_310K_traj1.pdb

The residue numbers use mature-protein numbering (the 31-residue signalling peptide is removed, so full-sequence 225 → 194):

Token	Mature no.	Full-sequence no.	Meaning
194	194	225 (H225)	Histidine deprotonated to the HIE tautomer
155	155	186	Legacy token — no proton removed here

Note on 155: a vestige of an earlier convention used when two histidine protons were removed. None of the current trajectories remove a proton at residue 155; the token is kept only for filename continuity and can be ignored. Consider dropping it from future runs to avoid confusion.

Trajectories

Run date	Trajectories	Count
2025-05-19	traj1–5, traj7–10	9
2025-05-22	traj6	1
2025-06-27	traj11, traj13–15, traj17–20	8
2025-07-01	traj21–23, traj27–30	7
2025-07-04	traj24, traj26	2
2026-04-22	traj12, traj16, traj25	3

Total: 30 trajectories, numbered traj1–traj30

Recoverability analysis

To test whether enzymes driven into a deactivated state can recover active-state behaviour, the medoid structure of each deactivated-range run was used to seed a fresh simulation with the pH reassigned to 4.6 (within the active range).

• Deactivated range (source): pH 6.6–7.4 of the initial titration run
• Recovery condition: pH reassigned to 4.6, otherwise identical (wildtype, 0.1500 M, 310 K, 30 ns)
• Starting structures: the medoid of each of the 30 deactivated-range runs, stripped to protein only
• Replicates: one recovery trajectory (traj1) per medoid

Stored in two dated batches inside results_30ns_salting/:

results_30ns_salting/
├── Medoid_2026-03-23/
│   └── openmm-md/
└── Medoid_2026-04-20/
    └── openmm-md/

File naming convention

<source_run>_medoid_protein_only_<recovery_run>.pdb

Example: wildtype_center_box_0.1500M_7.4pH_310K_traj9_medoid_protein_only_0.1500M_4.6pH_310K_traj1.pdb

Segment	Meaning
wildtype_center_box_0.1500M_7.4pH_310K_traj9	Source (deactivated) run whose medoid was extracted
medoid_protein_only	Representative (medoid) structure, solvent/ions stripped
0.1500M_4.6pH_310K_traj1	Recovery run at reassigned pH 4.6

Source runs (deactivated range)

Source pH	Source trajectories	Medoids
6.6	traj1–3	3
6.8	traj1–3	3
7.0	traj1–3	3
7.2	traj1–3	3
7.4	traj1–18	18

Total: 30 medoids → 30 recovery trajectories (one traj1 each), split across the two Medoid_* batches.

TDGAL results (α-galactosidase variants)

A separate study applies the same pipeline to five α-galactosidase variants (TDGAL18, 20, 35, 63, 75) at the two endpoint pH values, 4.6 and 7.4. These are stored outside the wildtype tree, in TDGAL_results_30ns_salting/, across two dated batches.

TDGAL_results_30ns_salting/
├── 2025-05-28/
│   └── openmm-md/
└── 2025-06-09/
    └── openmm-md/

File naming convention

TDGAL<variant>_center_box_0.1500M_<pH>pH_310K_traj<N>.pdb

e.g. TDGAL18_center_box_0.1500M_4.6pH_310K_traj1.pdb

Trajectory matrix

Cells show the run date of each trajectory (— = not present):

Variant	pH	traj1	traj2	traj3
TDGAL18	4.6	—	2025-05-28	2025-05-28
TDGAL18	7.4	2025-05-28	2025-06-09	2025-06-09
TDGAL20	4.6	2025-06-09	2025-05-28	2025-05-28
TDGAL20	7.4	2025-05-28	2025-06-09	2025-06-09
TDGAL35	4.6	2025-05-28	2025-05-28	2025-05-28
TDGAL35	7.4	2025-05-28	2025-06-09	2025-05-28
TDGAL63	4.6	2025-06-09	2025-06-09	2025-05-28
TDGAL63	7.4	2025-05-28	2025-05-28	2025-05-28
TDGAL75	4.6	2025-05-28	2025-05-28	2025-05-28
TDGAL75	7.4	2025-05-28	2025-06-09	2025-06-09

Total: 29 trajectories (missing TDGAL18 pH 4.6 traj1).