SciFlow lab notebook · Shared read-only

Steered MD — Titin I27 riga Unfolding (SciFlow)

Pull a protein through a steered-molecular-dynamics unfolding experiment and get back the force-extension curve, the rupture force, and the trajectory you can spin in 3D.

SMD

Overview Methods & provenance Results Raw artifacts

Run date

2026-05-01 → 2026-05-15

Stages

7 7 completed

Pipeline

md_prep → md_run

Software

seqshare-namd-autonomous:latest

Outputs

220 files 3.2 GB

Overview

Pull a protein through a steered-molecular-dynamics unfolding experiment and get back the force-extension curve, the rupture force, and the trajectory you can spin in 3D. This demo runs the canonical titin I27 domain (Lu et al. 1998) as a calibration benchmark — same pulling protocol (5 Å/ns, spring constant k = 7) used for the lab's other SMD targets, so force measurements are comparable run-to-run. Built for biophysics and mechanobiology groups measuring protein mechanical stability, and for anyone who needs a reproducible SMD pipeline — solvation, equilibration, production NAMD, steered pull, and force analysis — without re-wiring it for every new target.

Methods & per-stage provenance

7 stages, 7 completed. Each stage below lists the parameters it ran with, the software the run recorded, and the files it produced.

Not recorded by this run
  • no figures rendered (no PNG/SVG outputs and no Plotly HTML figure could be extracted)
00 Structure Preparation md_prep 10 min completed
step: structure_preppdb id: 1TIT

Verbatim command / script not recorded in this run's stage record.

Container image: not recorded in this stage's run metadata Image digest: not recorded in this stage's run metadata Tool versions: openbabel 3.1.1, python 3.11.14, rdkit 2026.03.1, vmd 1.9.3
  • 1TIT_clean.pdbstructure · 126 KB
  • input_data_summary.htmlreport · 2 KB
  • metadata.jsondata · 1 KB
  • protein.pdbstructure · 110 KB
  • structure_report.htmlreport · 3 KB
01 Protein PSF md_prep 3 s completed
step: protein_psfauto disulfides: Truefirst patch: NTERlast patch: CTERtemplate version: 1.0

Verbatim command / script not recorded in this run's stage record.

Container image: not recorded in this stage's run metadata Image digest: not recorded in this stage's run metadata Tool versions: openbabel 3.1.1, python 3.11.14, rdkit 2026.03.1, vmd 1.9.3
1TIT_clean.pdb: 4ac10bd5009c… _parent_info.json: 4b5dac4ace59… metadata.json: f4f186315f51… protein.pdb: 7ffe0f90c9bc… structure_report.html: fcccc5c298af…
  • generate_psf.tclscript · 891 B
  • protein.pdbstructure · 106 KB
  • protein.psftopology · 321 KB
  • psf_report.htmlreport · 5 KB
  • vmd_output.loglog · 30 KB
02 Solvation md_prep 1.0 h completed
step: solvationbox padding: 12salt concentration: 0.15water model: TIP3Ptemplate version: 1.3smd elongation: onsmd pull distance: 200

Verbatim command / script not recorded in this run's stage record.

Container image: not recorded in this stage's run metadata Image digest: not recorded in this stage's run metadata Tool versions: openbabel 3.1.1, python 3.11.14, rdkit 2026.03.1, vmd 1.9.3
1TIT_clean.pdb: 4ac10bd5009c… generate_psf.tcl: 74893f3935c1… metadata.json: f4f186315f51… protein.pdb: 6110fe7574f2… protein.psf: 134e87ebc358… psf_report.html: 9937088b9ac4… structure_report.html: fcccc5c298af… vmd_output.log: f1fb82f45b7e…
  • .smd_elongation_axisSMD_ELONGATION_AXIS · 1 B
  • .water_modelWATER_MODEL · 5 B
  • geometry_trace.jsondata · 646 B
  • solvate.tclscript · 9 KB
  • solvated.pdbstructure · 5.8 MB
  • solvated.psftopology · 7.4 MB
  • solvated.xsccell · 177 B
  • solvation_report.htmlreport · 6 KB
  • vmd_output.loglog · 179 KB
03 Minimization md_run 2.9 h completed
step: minimizationtemplate version: 1.5

Verbatim command / script not recorded in this run's stage record.

Container image: seqshare-namd-autonomous:latest Image digest: not recorded in this stage's run metadata Tool versions: python 3.10.12, vmd 1.9.3 Tool versions (probe failed): namd — the run recorded probe output that contains no version string
  • FFTW_NAMD_2.14_Linux-x86_64-multicore.txttext · 1 KB
  • min_stage1.coorcoordinates · 1.8 MB
  • min_stage1.loglog · 8.5 MB
  • min_stage1.namdconfig · 2 KB
  • min_stage1.stderrSTDERR · 0 B
  • min_stage1.velvelocities · 1.8 MB
  • min_stage1.xsccell · 172 B
  • min_stage2.coorcoordinates · 1.8 MB
  • min_stage2.loglog · 8.5 MB
  • min_stage2.namdconfig · 1 KB
  • min_stage2.stderrSTDERR · 0 B
  • min_stage2.velvelocities · 1.8 MB
  • min_stage2.xsccell · 172 B
  • minimization_report.htmlreport · 13 KB
  • minimized.coorcoordinates · 1.8 MB
  • minimized.pdbstructure · 5.8 MB
  • minimized.psftopology · 7.4 MB
  • minimized.xsccell · 172 B
04 Equilibration md_run 33 min completed
step: equilibrationtemplate version: 1.3

Verbatim command / script not recorded in this run's stage record.

Container image: seqshare-namd-autonomous:latest Image digest: not recorded in this stage's run metadata Tool versions: python 3.10.12, vmd 1.9.3 Tool versions (probe failed): namd — the run recorded probe output that contains no version string
  • equil_colvars.inIN · 1 KB
  • equilibrated.coorcoordinates · 1.8 MB
  • equilibrated.pdbstructure · 5.8 MB
  • equilibrated.psftopology · 7.4 MB
  • equilibrated.velvelocities · 1.8 MB
  • equilibrated.xsccell · 278 B
  • equilibration_report.htmlreport · 19 KB
  • minimized.coorcoordinates · 1.8 MB
  • npt_restrained.colvars.stateSTATE · 339 B
  • npt_restrained.colvars.trajTRAJ · 6 KB
  • npt_restrained.coorcoordinates · 1.8 MB
  • npt_restrained.dcdtrajectory · 88.2 MB
  • npt_restrained.loglog · 92 KB
  • npt_restrained.namdconfig · 2 KB
  • npt_restrained.restart.colvars.stateSTATE · 339 B
  • npt_restrained.restart.colvars.state.oldOLD · 337 B
  • npt_restrained.restart.coorcoordinates · 1.8 MB
  • npt_restrained.restart.velvelocities · 1.8 MB
  • npt_restrained.restart.xsccell · 281 B
  • npt_restrained.stderrSTDERR · 0 B
  • npt_restrained.velvelocities · 1.8 MB
  • npt_restrained.xsccell · 280 B
  • npt_unrestrained.colvars.stateSTATE · 339 B
  • npt_unrestrained.colvars.trajTRAJ · 6 KB

+ 22 more output file(s) — see Raw artifacts.

05 SMD md_run 16.9 h completed
step: smdautonomous: Trueautonomous resource class: gpuautonomous compute image: seqshare-namd-autonomous:latestautonomous cpus: 8replicas: 3template version: 1.1smd steps: 5000000

Verbatim command / script not recorded in this run's stage record.

Container image: seqshare-namd-autonomous:latest Image digest: not recorded in this stage's run metadata Tool versions: python 3.10.12, vmd 1.9.3 Tool versions (probe failed): namd — the run recorded probe output that contains no version string
  • extension_time.htmlreport · 32 KB
  • force_extension.htmlreport · 33 KB
  • force_time.htmlreport · 33 KB
  • r1__extension_time.htmlreport · 32 KB
  • r1__force_extension.htmlreport · 31 KB
  • r1__force_time.htmlreport · 31 KB
  • r1__smd.coorcoordinates · 1.8 MB
  • r1__smd.dcdtrajectory · 881.5 MB
  • r1__smd.loglog · 8.9 MB
  • r1__smd.namdconfig · 2 KB
  • r1__smd.pdbstructure · 5.8 MB
  • r1__smd.psftopology · 7.4 MB
  • r1__smd.restart.coorcoordinates · 1.8 MB
  • r1__smd.restart.coor.oldOLD · 1.8 MB
  • r1__smd.restart.velvelocities · 1.8 MB
  • r1__smd.restart.vel.oldOLD · 1.8 MB
  • r1__smd.restart.xsccell · 193 B
  • r1__smd.restart.xsc.oldOLD · 193 B
  • r1__smd.stderrSTDERR · 0 B
  • r1__smd.velvelocities · 1.8 MB
  • r1__smd.xsccell · 192 B
  • r1__smd_force.csvtable · 3.9 MB
  • r1__smd_report.htmlreport · 4 KB
  • r1__smd_setup.jsondata · 793 B

+ 63 more output file(s) — see Raw artifacts.

06 SMD Analysis md_prep 1.0 h completed
step: smd_analysis

Verbatim command / script not recorded in this run's stage record.

Container image: not recorded in this stage's run metadata Image digest: not recorded in this stage's run metadata Tool versions: openbabel 3.1.1, python 3.11.14, rdkit 2026.03.1, vmd 1.9.3
1TIT_clean.pdb: 4ac10bd5009c… FFTW_NAMD_2.14_Linux-x86_64-multicore.txt: 53421dfcb361… equil_colvars.in: d6906a348eb2… equilibrated.coor: e2643b9e5aac… equilibrated.pdb: 85c72fcbc6f1… equilibrated.psf: 2b278181e5cd… equilibrated.vel: 684765e3f666… equilibrated.xsc: 4891251d0ae4…
  • contact_map_r1.htmlreport · 49 KB
  • contact_map_r2.htmlreport · 49 KB
  • contact_map_r3.htmlreport · 49 KB
  • contact_map_replica_1.htmlreport · 5 KB
  • force_extension_mean.csvtable · 17 KB
  • force_extension_overlay.htmlreport · 92 KB
  • hbonds_mean.htmlreport · 6 KB
  • hbonds_vs_extension_r1.htmlreport · 4 KB
  • hbonds_vs_extension_r2.htmlreport · 4 KB
  • hbonds_vs_extension_r3.htmlreport · 4 KB
  • hbonds_vs_extension_replica_1.htmlreport · 3 KB
  • mean_force_profile.htmlreport · 24 KB
  • native_contacts_mean.htmlreport · 6 KB
  • native_contacts_r1.htmlreport · 5 KB
  • native_contacts_r2.htmlreport · 5 KB
  • native_contacts_r3.htmlreport · 5 KB
  • native_contacts_replica_1.htmlreport · 3 KB
  • raw_vs_smoothed.htmlreport · 61 KB
  • rgyr_mean.htmlreport · 6 KB
  • rgyr_vs_extension_r1.htmlreport · 4 KB
  • rgyr_vs_extension_r2.htmlreport · 4 KB
  • rgyr_vs_extension_r3.htmlreport · 4 KB
  • rgyr_vs_extension_replica_1.htmlreport · 3 KB
  • salt_bridges_mean.htmlreport · 5 KB

+ 26 more output file(s) — see Raw artifacts.

Results

No static figure could be embedded in this notebook — this run recorded no PNG/SVG output, and no interactive plot could be exported to a static image. Any figures this run produced are listed among the raw artifacts below and remain viewable in the project itself.

Raw artifacts

220 output files produced across all stages (3.2 GB total). This report is self-contained; structures and trajectories are listed below for reference.