lysozyme_10ns

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A complete run, start to finish

This is hen egg-white lysozyme — PDB 1AKI, the orthorhombic form at 1.5 Å — simulated for 10 nanoseconds in explicit water on an Apple M1 Max. It is the same three steps the two tabs either side of this one describe: configure a run, run the single file it hands you, upload what comes back.

Nothing here is illustrative. The tables are read out of the run's own config.json, the terminal blocks are the bytes the run printed, and every panel further down is built from the results file by the code that renders an upload. If the Analysis tab breaks, this page breaks with it.

Prepared

1AKI loaded from the RCSB, hydrogens added at pH 7.4, solvated in a dodecahedral box with 1.2 nm padding and neutralised to 0.15 M NaCl. 2,194 solute atoms became 19,433 with water.

Ran

One .command file, run from Terminal. It benchmarked the machine's platforms, minimised, heated to 310 K, equilibrated for 200 ps while releasing restraints, then produced 10 ns at 4 fs with hydrogen-mass repartitioning.

Analysed

The run packed a .fxa results file: metrics, a decimated trajectory and the topology to view it against. That file is committed to the repository, and it is what this page is rendering.

Reproduce it: the bundle is in the repository at examples/lysozyme_10ns/flexappeal_lysozyme_10ns.command. Download it, chmod +x it, and run it. The first run installs the environment; after that it goes straight to simulating.

What it looked like on the machine

Captured from the terminal while this ran, not re-created afterwards: these are the bytes the scripts wrote, replayed through the same library that produced them. The bars are caught mid-stage on purpose — a finished bar sits at 100% with its live readouts gone, which is the one state not worth showing. The one edit is that home directories are shortened to ~.

1 Running `run.py`

Startup, and the platform benchmark that picks OpenCL

╭──────────────────────────────────────────────────────────────────────────────────────╮
│  lysozyme_10ns                                                                       │
│  10.0 ns · amber14-all.xml · tip3p in a dodecahedron, 1.2 nm padding, 0.15 M Na+Cl-  │
│                                                                                      │
│  FlexAppeal 0.1.0   OpenMM 8.5.2.dev-36a30cb   arm64 · 10 cores · 68.7 GB RAM        │
╰──────────────────────────────────────────────────────────────────────────────────────╯
→ preparing the structure
ℹ added hydrogens at pH 7.4
✓ prepared: 2194 atoms, 207 residues
ℹ wrote prepared.pdb
✓ solvated: 19433 atoms, 5811 waters  1s
ℹ wrote solvated.pdb
✓ system: 19433 particles, 18392 constraints, 6 forces  0s
⠼   relaxing initial clashes -294,371 kJ/mol 589 iterations 166.2 MB rss · 34.3 GB free · 0 B swap 0:00:04
✓ clashes relaxed  4s
ℹ restrained 1001 atoms at 1000.0 kJ/mol/nm²
ℹ platforms available: Reference, CPU, OpenCL
→ benchmarking 2 platforms (CPU, OpenCL)
ℹ   CPU            29.5 ns/day
⚠ OpenCL does not support mixed precision here; using single
ℹ   OpenCL        206.5 ns/day
✓ using OpenCL at 206.5 ns/day

Energy minimisation: a spinner, not a bar -- OpenMM's iteration count is not monotonic

ℹ   OpenCL        206.5 ns/day
✓ using OpenCL at 206.5 ns/day
⚠ OpenCL does not support mixed precision here; using single
⠼   minimising -324,795 kJ/mol 2,891 iterations 254.6 MB rss · 34.1 GB free · 0 B swap 0:00:18

Heating, 50 K to 310 K

⚠ OpenCL does not support mixed precision here; using single
✓ minimised over 4,966 iterations: -294,354 → -325,460 kJ/mol  31s
→ heating 50.0 → 310.0 K over 100.0 ps
  heating ━━━━━━━━━━━━╺━━━━━━━  60%   206 K 317.1 MB rss · 33.7 GB free · 0 B swap 0:00:19 00:14

Equilibration, with the positional restraints released in stages

→ heating 50.0 → 310.0 K over 100.0 ps
✓ heated to 310.0 K  33s
→ equilibrating for 200.0 ps
  equilibrating ━━━━━━━━━━╺━━━━━━━━  54%   restraint 100 kJ/mol/nm² 433.4 MB rss · 34.2 GB free · 0 B swap 0:00:41 00:37

Production: ns/day, resident memory, free memory and swap, all live

→ equilibrating for 200.0 ps
✓ equilibrated  1m22s
→ producing 10.0 ns (2,500,000 steps)
  producing ━━━━━━━━━╸━━━━━━━━━━  48%   200 ns/day 4.3 GB rss · 32.3 GB free · 0 B swap 0:34:37 --:--

The closing summary

  producing ━━━━━━━━━━━━━━━━━━━━ 100%   204 ns/day 8.3 GB rss · 32.3 GB free · 0 B swap 1:09:12 00:00
✓ production complete in 1.17 h (204.3 ns/day)
✓ all runs complete
wall time    1h13m                                                                                       
output       ~/Documents/Vibe_Coding/FlexAppeal/examples/lysozyme_10ns/run/flexappeal_output
peak memory  8.3 GB resident                                                                             
swap         0 B added by this run                                                                       
ℹ next: run  ./analyse.py  to build the .fxa results file for the Analysis tab

The memory figures are the reason they are there. A run that spills out of RAM into swap does not slow down a little, it slows by an order of magnitude, and nothing else on screen would tell you. This one never swapped.

2 Then `analyse.py`

The second script reads the trajectory back, computes the metrics, and packs the results file. One bar carries all of them, relabelled with whichever metric is in flight — SASA and the contact map are the slow ones.

Analysing: one bar across every metric, relabelled as it goes

→ loading trajectory.xtc
✓ 1000 frames, 1960 atoms, 10.0 ns
ℹ re-imaged molecules (undoing periodic wrapping)
  contact map ━━━━━━━━━━━━━━━━━━━━╸━━━━━  80% 693.9 MB rss · 36.1 GB free 0:01:18

Packing the results file the Analysis tab reads

  conformational clustering ━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 768.1 MB rss · 36.2 GB free 0:01:19
ℹ packing 500 frames of 1960 atoms (standard tier, stride 2)
✓ wrote lysozyme_10ns.fxa (5.2 MB)
✓ 1 results file(s) ready

That .fxa is the file every panel below is rendered from.

Every setting this run used

All 115 options, grouped as the Prepare tab groups them and read from the registry rather than written out here, so a new option appears the day it is added. Values changed from the default are marked •; the rest are defaults, which for a reference run is worth being able to see rather than having to assume.

🏷️ Job 4 options, 2 changed

	Setting	Value
•	Job name	lysozyme_10ns
•	Description	Hen egg-white lysozyme (PDB 1AKI), 10 ns unrestrained NPT production in explicit TIP3P water. The reference example shipped with FlexAppeal.
	Author	—
	Output directory	./flexappeal_output

🧬 Input structure 16 options

	Setting	Value	OpenMM
	Structure source	upload
	Structure file	None
	PDB ID	—
	UniProt accession	—
	Assembly	asymmetric
	Model	1
	Chains to keep	*
	Alternate locations	occupancy
	Keep crystallographic waters	yes
	Water shell radius	5.0 Å
	Heteroatoms to keep	—
	Discard input hydrogens	yes
	Disulfide bonds	auto
	Disulfide detection cutoff	2.5 Å
	Disulfide pairs	—
	Terminal caps	charged

🩹 Structure repair 8 options

Setting	Value	OpenMM
Build missing residues	yes	`findMissingResidues`
Longest gap to build	25 residues
Build missing terminal residues	no
Replace non-standard residues	yes	`replaceNonstandardResidues`
Add missing heavy atoms	yes	`addMissingAtoms`
pH	7.4	`addMissingHydrogens`
Protonation overrides	—
Mutations	—	`applyMutations`

⚛️ Force field 11 options

Setting	Value	OpenMM
Protein force field	amber14-all.xml	`ForceField`
Water model	tip3p
Solvent treatment	explicit
Implicit solvent model	implicit/gbn2.xml
Implicit salt concentration	0.15 M
Solute dielectric	1.0
Solvent dielectric	78.5
Small-molecule force field	openff-2.2.1	`SystemGenerator`
Ligand partial charges	am1bcc
System contains ligands or cofactors	no
Additional force-field XML	None

💧 Solvation and box 9 options

Setting	Value	OpenMM
Box shape	dodecahedron	`addSolvent`
Box sizing	padding
Solvent padding	1.2 nm
Box vectors	— nm
Number of waters	10000
Positive ion	Na+
Negative ion	Cl-
Ionic strength	0.15 M
Neutralise the system	yes

🧱 Membrane 5 options

Setting	Value	OpenMM
Embed in a lipid bilayer	no	`addMembrane`
Lipid	POPC
Orientation	opm
Membrane centre (z)	0.0 nm
Minimum padding	1.0 nm

🔧 System 11 options

Setting	Value	OpenMM
Non-bonded method	PME	`PME`
Non-bonded cutoff	1.0 nm	`createSystem`
Use a switching function	no
Switching distance	0.9 nm
Ewald error tolerance	0.0005
Bond constraints	HBonds	`HBonds`
Rigid water	yes
Hydrogen mass repartitioning	yes	`createSystem`
Hydrogen mass	1.5 amu
Remove centre-of-mass motion	yes	`CMMotionRemover`
Long-range dispersion correction	yes	`setUseDispersionCorrection`

⏱️ Integrator 8 options

Setting	Value	OpenMM
Integrator	LangevinMiddle	`LangevinMiddleIntegrator`
Temperature	310.0 K
Friction coefficient	1.0 ps⁻¹
Timestep	4.0 fs
Error tolerance	0.0001
Add an Andersen thermostat	no	`AndersenThermostat`
Collision frequency	1.0 ps⁻¹
Random seed	0

🎈 Pressure control 7 options

Setting	Value	OpenMM
Pressure control	MonteCarlo	`MonteCarloBarostat`
Pressure	1.0 bar
Barostat interval	25 steps
Surface tension	0.0 bar·nm
XY coupling	XYIsotropic
Z coupling	ZFree
Per-axis pressure	1.0, 1.0, 1.0 bar

📌 Restraints 5 options

Setting	Value	OpenMM
Restrain the solute during equilibration	yes	`CustomExternalForce`
Restrained atoms	protein_heavy
Restraint force constant	1000.0 kJ/mol/nm²
Release schedule	1000, 500, 100, 10, 0 kJ/mol/nm²
Distance restraints	—

📈 Protocol 10 options, 2 changed

	Setting	Value	OpenMM
	Energy minimisation	yes	`minimizeEnergy`
	Minimisation tolerance	10.0 kJ/mol/nm
	Maximum minimisation steps	0
	Heating	100.0 ps
	Starting temperature	50.0 K
	Heating stages	5
•	Equilibration	200.0 ps
•	Production	10.0 ns
	Replicates	1
	Replicate seeds	sequential

💾 Output and reporting 10 options

Setting	Value	OpenMM
Trajectory format	xtc	`XTCReporter`
Trajectory write interval	10.0 ps
Atoms to save	protein_ligand
Custom atom selection	—
Wrap coordinates into the box	yes
Energy log interval	10.0 ps
Energy log fields	step, time, potentialEnergy, kineticEnergy, totalEnergy, temperature, volume, density, speed, progress, remainingTime	`StateDataReporter`
Checkpoint interval	100.0 ps	`CheckpointReporter`
Save serialised system	yes
Save the solvated structure	yes

🚀 Platform and performance 6 options

Setting	Value	OpenMM
Compute platform	auto	`getPlatformByName`
Precision	mixed
CPU threads	0
Deterministic forces	no
Device index	—
Refuse to start if memory is short	yes

📊 Analysis 5 options

	Setting	Value	OpenMM
	Metrics to compute	rmsd, rmsf, rgyr, sasa, dssp, hbonds, contacts, pca, clusters
	Reference structure	first
	Alignment selection	backbone
	Custom measurements	—
	Results file size	standard

The analysis, exactly as the Analysis tab renders it

Hen egg-white lysozyme (PDB 1AKI), 10 ns unrestrained NPT production in explicit TIP3P water. The reference example shipped with FlexAppeal.

amber14-all.xml / tip3p · 310.0 K · 4.0 fs · OpenCL · OpenMM 8.5.2.dev-36a30cb · 1aki.pdb

Simulated

10.0ns

Frames

1,000

500 packed for viewing

Final RMSD

0.94Å

mean of the last 10% of frames

Radius of gyration

14.29Å

trajectory mean

Hydrogen bonds

194

occupancy > 10%

Helix content

40%

trajectory mean

Throughput

204ns/day

OpenCL

Wall time

1.2h

Structure

The decimated trajectory, 500 frames of 1960 atoms. Press play, or scrub the frame slider — the plots below highlight the frame you are on.

Loading the structure…

RMSD

How far the structure has moved from its reference. A plateau means the trajectory has settled; a steady climb means it has not.

Radius of gyration

Global compactness. A rise suggests unfolding or expansion.

Per-residue fluctuation

Which parts of the molecule move. Peaks are usually loops and termini.

Solvent exposure

Total solvent-accessible surface area over time.

Secondary structure content

Helix and sheet content over the trajectory.

Secondary structure timeline

Per-residue assignment at every frame. Vertical stripes are transient melting; horizontal bands are stable elements.

Contact map

How often each residue pair is in contact across the whole trajectory.

Essential dynamics

The two dominant collective motions, with each frame coloured by time. Distinct clouds mean distinct conformational states.

Conformational clusters

Representative states found by RMSD clustering.

Convergence

Each measure on its own axis. Energies, temperature and density differ by orders of magnitude, so sharing a plot between any two of them would make their alignment arbitrary and any apparent correlation fictional.

Ask something else

Compute a metric the run did not, or restrict one to part of the molecule. This runs on the server against the trajectory packed in your results file, so it is bounded: one job at a time, and a size limit. This is a standard-tier file — it carries a thinned trajectory, so answers here are coarser than the panels above. Rebuild with the full tier for the richest re-analysis.

Metrics

RMSD against the reference Per-residue fluctuation Radius of gyration Solvent-accessible surface area Secondary structure Hydrogen bonds Residue contact map Principal component analysis Distance between two selections

Atom selection

MDTraj selection syntax. protein, name CA, chainid 0 and backbone, resname BEN. Use resSeq for the residue numbers you see in the PDB — resid is a zero-based index into the topology, so resid 195 is rarely residue 195.

Run details

Every value is read from the results file's manifest.
Simulated time	10.000 ns
Frames analysed	1,000
Frames packed	500 (standard tier)
Force field	amber14-all.xml
Water model	tip3p
Temperature	310.0 K
Timestep	4.0 fs
Platform	OpenCL
Throughput	204.33 ns/day
Wall time	1.17 h
OpenMM	8.5.2.dev-36a30cb
FlexAppeal	0.1.0
Machine	Darwin 25.5.0 (arm64)
Metrics computed	rmsd, rmsf, rgyr, sasa, dssp, hbonds, contacts, pca, clusters

Everything above is generated from the results file this run produced, by the same code that renders an upload. Try it with your own: prepare a run, or upload a results file.

A complete run, start to finish

Prepared

Ran

Analysed

What it looked like on the machine

1 Running run.py

2 Then analyse.py

Every setting this run used

The analysis, exactly as the Analysis tab renders it

lysozyme_10ns

Structure

RMSD

Radius of gyration

Per-residue fluctuation

Solvent exposure

Secondary structure content

Secondary structure timeline

Contact map

Essential dynamics

Conformational clusters

Convergence

Ask something else

Run details

1 Running `run.py`

2 Then `analyse.py`