Protein preparation, docking, simulation & ensemble validation
Prepare structures, dock ligands, set up simulations, and score structural ensembles against experimental data (NMR, SAXS).
20 project-authored proposals · taxonomy v1.1 · 0 new benchmark runs. Verifiers and partial-credit rules below are designs, not executed results.
- Typical applications
- Maestro · MOE · AmberTools
- Class GUI-need label
HY· Hybrid
Task proposals · 20
Expand to inspect the complete original wording and proposed checks. Original proposal text remains English in both interfaces.
R08.05.01.03-T01 Prepare HIV protease 1HSG in Maestro with a specified catalytic aspartate protonation
Original instruction
In Maestro run the Protein Preparation Workflow on input/1hsg.pdb: assign bond orders, add hydrogens, fill missing side chains, Epik states for MK1 at pH 7±2, H-bond optimization at pH 7.0, delete waters beyond 5 Å of the ligand, then set Asp25 of chain A protonated (ASH) and chain B charged before restrained minimization (OPLS4, 0.3 Å). Export output/prepared.mae.
- Platforms
win· Windowsmac· macOSlin· Linux- Applications
- Schrödinger Maestro
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & formsvis· Visual judgment- Work product
WP04· 3D/spatial model- Conditions
licensed· Licensed pro app- Proposed difficulty
- 3 / 5
Proposed verifier
prepared.mae: A:Asp25 = ASH and B:Asp25 = ASP; His tautomers equal the reference workflow; heavy-atom RMSD to input <0.3 Å; only waters within 5 Å remain. Job records must show launch from Maestro panels (others are detected); the Schrödinger Python API and command-line utilities are absent from PATH.
Proposed partial credit
25% bond orders/H/side chains; 35% Asp25 protonation states; 20% His states; 20% waters and minimization.
R08.05.01.03-T02 Generate a Glide grid on the co-crystal ligand, redock it and rank five ligands
Original instruction
In Maestro, using the prepared 1HSG in input/prepared.mae, generate a receptor grid centred on MK1 (inner box 10 Å, outer 20 Å), prepare input/ligands.sdf (5 ligands plus MK1) with LigPrep, dock with Glide SP, and export output/poses.maegz and output/scores.csv ranked by docking score.
- Platforms
win· Windowsmac· macOSlin· Linux- Applications
- Schrödinger Maestro · Glide
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & formsvis· Visual judgment- Work product
WP07· Simulation result- Conditions
licensed· Licensed pro app- Proposed difficulty
- 4 / 5
Proposed verifier
Grid centre within 1 Å of MK1 centroid with stated box sizes; MK1 redock heavy-atom RMSD <2.0 Å; top-ranked ligand ID equals the reference run; Maestro-launched job records required. The Schrödinger Python API and command-line utilities are absent from PATH, and job records detect any job not launched from a Maestro panel.
Proposed partial credit
25% grid; 15% LigPrep; 35% redock RMSD; 25% ranking.
R08.05.01.03-T03 Find the binding site with Site Finder and dock ten ligands in MOE
Original instruction
In MOE run QuickPrep on input/target.pdb, use Site Finder and pick the site whose residues best match input/site_residues.txt, place dummies there, and dock input/ligands10.sdf (Triangle Matcher, London dG, GBVI/WSA dG rescoring, 5 poses). Export the top pose per ligand with scores to output/top_poses.sdf.
- Platforms
win· Windowsmac· macOS- Applications
- MOE
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & formsvis· Visual judgment- Work product
WP07· Simulation result- Conditions
licensed· Licensed pro app- Proposed difficulty
- 3 / 5
Proposed verifier
Dummy-atom centroid within 2 Å of the reference site centre; the included reference ligand redocks with RMSD <2 Å; top_poses.sdf holds 10 records with S scores matching a reference rerun within 0.5. The MOE SVL console and moebatch are disabled; docking must run from the MOE panels.
Proposed partial credit
20% preparation; 30% correct site; 30% reference redock; 20% export.
R08.05.01.03-T04 Prepare receptor and ligand in AutoDockTools, set the grid box visually, and redock with Vina
Original instruction
In AutoDockTools prepare input/rec.pdb (polar H, Gasteiger charges, merge non-polar H) and input/lig.pdb (torsion tree), save PDBQTs, and set the grid box in the GUI to enclose the pocket residues in input/pocket.txt with spacing 0.375 Å. Write output/conf.txt, run Vina (exhaustiveness 16), and save output/out.pdbqt.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- AutoDockTools · AutoDock Vina
- Interfaces
desk· Desktop GUIterm· Terminal- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
drag· Drag & dropclick· Point & clickvis· Visual judgmentgeom· Precise geometry- Work product
WP07· Simulation result- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
Box encloses all pocket-residue atoms with ≤8 Å margin and volume ≤27,000 ų; receptor PDBQT charges equal Gasteiger reference; best pose heavy-atom RMSD to crystal <2.0 Å. The prepare_receptor/prepare_ligand scripts, Meeko and Open Babel are absent and ADT's Python shell is disabled, so PDBQTs must be written from ADT.
Proposed partial credit
25% receptor/ligand PDBQT; 35% grid box; 40% redock RMSD.
R08.05.01.03-T05 Embed a GPCR in a POPC/cholesterol bilayer with CHARMM-GUI Membrane Builder
Original instruction
Using a CHARMM-GUI test account, run Membrane Builder on input/gpcr_oriented.pdb (OPM orientation): POPC:CHOL 3:1 in both leaflets, about 80×80 Å, 22.5 Å water thickness, 0.15 M KCl, CHARMM36m, GROMACS output. Download the archive to output/charmm-gui.tgz.
- Platforms
web· Any OS (web)- Applications
- CHARMM-GUI
- Interfaces
brow· Browser- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clicktype· Text & forms- Work product
WP06· Code/engineering- Conditions
long· Long-horizon- Proposed difficulty
- 4 / 5
Proposed verifier
From the archive: lipid ratio POPC:CHOL 3:1 ±5% per leaflet; box x/y 80±5 Å; K+/Cl− giving 0.15±0.01 M plus neutralization; protein orientation within 5° of input; GROMACS topology and mdp files present. The test account is issued no CHARMM-GUI API token, so the build must run in the web session, and the archive's step logs must come from it.
Proposed partial credit
25% lipid composition; 20% box size; 20% ions; 35% orientation and GROMACS files.
R08.05.01.03-T06 Control: build the same solvated system with Schrödinger's command-line System Builder
Original instruction
Control pair of T07. Using Schrödinger's command-line tools only ($SCHRODINGER/utilities/system_builder with a .csb/.msj file), solvate input/complex_prepped.mae with TIP3P in an orthorhombic 10 Å buffer box with minimized volume, neutralize, add 0.15 M NaCl with OPLS4, and write output/system-out.cms.
- Platforms
lin· Linuxmac· macOS- Applications
- Schrödinger Suite CLI
- Interfaces
term· Terminal- GUI need · task setting
CL· CLI-sufficient- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
code· Code & commands- Work product
WP06· Code/engineering- Conditions
licensed· Licensed pro app- Proposed difficulty
- 2 / 5
Proposed verifier
Same checker as T07: orthorhombic box ≥ solute extent + 20 Å, net charge 0, NaCl for 0.15 M ±2 ions, OPLS4, solute coordinates unchanged. Scored as the CLI control of T07.
Proposed partial credit
30% box; 40% ions and charge; 30% force field and solute preserved.
R08.05.01.03-T07 Build a solvated, neutralized simulation box for a complex in Maestro System Builder
Original instruction
In Maestro System Builder load input/complex_prepped.mae, solvate with TIP3P in an orthorhombic box with 10 Å buffer and minimized volume, neutralize with Na+/Cl−, add 0.15 M NaCl, use OPLS4, and write output/system-out.cms.
- Platforms
win· Windowsmac· macOSlin· Linux- Applications
- Schrödinger Maestro · Desmond
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & forms- Work product
WP06· Code/engineering- Conditions
licensed· Licensed pro app- Proposed difficulty
- 3 / 5
Proposed verifier
CMS parsed: orthorhombic box ≥ solute extent + 20 Å; net charge 0; NaCl count matches 0.15 M for the water count ±2; OPLS4 force field; solute coordinates unchanged. The Schrödinger Python API and command-line utilities are absent from PATH, and job records detect any job not launched from a Maestro panel.
Proposed partial credit
30% box shape/buffer; 40% ions; 30% force field and solute preserved.
R08.05.01.03-T08 Run a 50-ligand Vina screen in PyRx and report the top five
Original instruction
In PyRx load the receptor input/rec.pdb and the 50 ligands in input/library.sdf, minimize ligands with UFF, run the Vina wizard with the box around input/pocket.txt residues (exhaustiveness 8), and export all results to output/screen.csv. Write the top five ligand IDs to output/answer.json.
- Platforms
win· Windowsmac· macOSlin· Linux- Applications
- PyRx · AutoDock Vina
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clickdrag· Drag & drop- Work product
WP07· Simulation result- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
screen.csv holds all 50 ligands with affinities; box centre within 2 Å of pocket centroid; top-5 overlaps the reference top-5 in ≥4 of 5 (stochastic tolerance), with the reference best ligand included.
Proposed partial credit
20% ligands prepared; 20% box; 30% complete results; 30% top-five overlap.
R08.05.01.03-T09 Recover a crystal pose with Induced Fit Docking where rigid docking fails
Original instruction
Glide SP places input/bulky_ligand.sdf >4 Å from its crystal pose in input/receptor_other_ligand.mae because of a closed side chain. In Maestro run Induced Fit Docking (standard protocol, refine residues within 5 Å, Glide SP redock), and export the best pose by IFD score to output/ifd_best.mae with the score in output/answer.json.
- Platforms
win· Windowsmac· macOSlin· Linux- Applications
- Schrödinger Maestro · Glide · Prime
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & formsvis· Visual judgment- Work product
WP07· Simulation result- Conditions
licensed· Licensed pro applong· Long-horizon- Proposed difficulty
- 5 / 5
Proposed verifier
Best pose ligand heavy-atom RMSD <2.0 Å to the crystal (receptor aligned on pocket Cα); IFD score equals the job output; IFD job records show Maestro launch and the stated refinement radius. The Schrödinger Python API and command-line utilities are absent from PATH, and job records detect any job not launched from a Maestro panel.
Proposed partial credit
25% IFD settings; 25% job completed; 50% pose RMSD (full <2 Å, zero >4 Å).
R08.05.01.03-T10 Run Dock Prep on a complex in UCSF Chimera and charge the ligand with AM1-BCC
Original instruction
In UCSF Chimera open input/complex.pdb, run Dock Prep (delete solvent and ions, complete incomplete side chains with Dunbrack rotamers, add hydrogens), assign AM1-BCC charges to the ligand with net charge −1, and save output/receptor.mol2 and output/ligand.mol2.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- UCSF Chimera
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & forms- Work product
WP04· 3D/spatial model- Conditions
- None declared
- Proposed difficulty
- 2 / 5
Proposed verifier
No waters or ions in receptor; listed incomplete side chains completed; ligand total partial charge −1.000±0.001 with AM1-BCC values within 0.02 of reference; Sybyl atom types present.
Proposed partial credit
25% solvent removed; 25% side chains; 20% hydrogens; 30% ligand charges.
R08.05.01.03-T11 Assign protonation states at pH 5.5 with MOE Protonate3D and report histidines
Original instruction
In MOE open input/enzyme.pdb, run Protonate3D at pH 5.5, 300 K, 0.1 M salt, and save output/prot.moe. Report the protonation state (HID, HIE or HIP) of the six histidines and the state of Glu35 and Glu172 in output/states.json.
- Platforms
win· Windowsmac· macOS- Applications
- MOE
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & forms- Work product
WP04· 3D/spatial model- Conditions
licensed· Licensed pro app- Proposed difficulty
- 3 / 5
Proposed verifier
states.json equal to the reference Protonate3D run at the stated conditions and consistent with prot.moe hydrogens; running at default pH 7.0 changes at least two states.
Proposed partial credit
60% six histidines (10 pts each); 20% two glutamates; 20% saved structure consistent.
R08.05.01.03-T12 Dock an acrylamide inhibitor covalently to EGFR Cys797 with CovDock
Original instruction
In Maestro use CovDock with input/egfr_prepared.mae and input/acrylamide_inhibitor.sdf: reactive residue Cys797, reaction Michael addition, pose prediction mode, grid centred on the hinge-bound co-crystal ligand. Export the top pose to output/covdock_best.mae.
- Platforms
win· Windowsmac· macOSlin· Linux- Applications
- Schrödinger Maestro · CovDock
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & formsvis· Visual judgment- Work product
WP07· Simulation result- Conditions
licensed· Licensed pro app- Proposed difficulty
- 5 / 5
Proposed verifier
Covalent bond present between Cys797 SG and the β-carbon (1.75–1.90 Å); ligand heavy-atom RMSD to the crystal covalent complex <2.5 Å; hinge H-bond to Met793 present. Maestro-launched job record required. The Schrödinger Python API and command-line utilities are absent from PATH, and job records detect any job not launched from a Maestro panel.
Proposed partial credit
20% CovDock setup; 30% covalent bond; 40% pose RMSD; 10% hinge contact.
R08.05.01.03-T13 Enumerate ionization states and tautomers for twelve ligands with LigPrep and Epik
Original instruction
In Maestro run LigPrep on input/ligs.smi (12 ligands) with Epik at pH 7.0±2.0, generate tautomers, retain specified chiralities and keep at most 4 states per ligand. Save output/ligprep.maegz and write the number of states per ligand to output/states.csv.
- Platforms
win· Windowsmac· macOSlin· Linux- Applications
- Schrödinger Maestro · LigPrep
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & forms- Work product
WP02· Records/table- Conditions
licensed· Licensed pro app- Proposed difficulty
- 3 / 5
Proposed verifier
Per-ligand state counts and the set of state SMILES equal the reference LigPrep run; specified stereocentres unchanged in every state; states.csv consistent with the output file.
Proposed partial credit
40% state counts; 40% state sets; 20% chirality retained.
R08.05.01.03-T14 Build a protein–ligand system with CHARMM-GUI and run a short NVT check in GROMACS
Original instruction
With a CHARMM-GUI test account, parameterize the ligand in input/complex.pdb with Ligand Reader & Modeler (CGenFF), build the complex in Solution Builder (cubic box, 10 Å buffer, 0.15 M KCl, CHARMM36m), download GROMACS inputs, then run the minimization and a 100 ps NVT equilibration locally. Report average temperature in output/answer.json.
- Platforms
web· Any OS (web)lin· Linux- Applications
- CHARMM-GUI · GROMACS
- Interfaces
brow· Browserterm· Terminal- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
HY· Hybrid- Interaction primitives
click· Point & clicktype· Text & formscode· Code & commands- Work product
WP07· Simulation result- Conditions
multiapp· Multi-app- Proposed difficulty
- 4 / 5
Proposed verifier
Topology includes ligand CGenFF parameters; KCl gives 0.15±0.01 M; NVT log completes 100 ps with average T 303.15±3 K and no LINCS warnings; answer equals gmx energy output within 0.5 K.
Proposed partial credit
25% ligand parameters; 25% system build; 30% minimization+NVT run; 20% temperature report.
R08.05.01.03-T15 Make two pocket side chains flexible for Vina docking in AutoDockTools
Original instruction
In AutoDockTools open input/rec.pdbqt, select Arg103 and Tyr105 of chain A as flexible residues, choose their rotatable bonds, and write output/rec_rigid.pdbqt and output/rec_flex.pdbqt.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- AutoDockTools
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clickvis· Visual judgment- Work product
WP04· 3D/spatial model- Conditions
- None declared
- Proposed difficulty
- 2 / 5
Proposed verifier
rec_flex.pdbqt contains exactly A:Arg103 and A:Tyr105 side chains with BEGIN_RES blocks and torsion counts equal to a reference ADT run's defaults; rec_rigid.pdbqt lacks those side-chain atoms beyond CA.
Proposed partial credit
50% correct residues flexible; 30% torsions; 20% rigid file consistent.
R08.05.01.03-T16 Build a pharmacophore hypothesis from five actives and screen a decoy set with Phase
Original instruction
In Maestro open input/actives.maegz (five aligned actives). With Phase develop a common-feature hypothesis with at least 4 features including one donor, one acceptor and one aromatic ring, then screen input/screen.maegz (10 actives hidden among 190 decoys). Save the hypothesis and output/hits.csv ranked by Phase screen score.
- Platforms
win· Windowsmac· macOSlin· Linux- Applications
- Schrödinger Maestro · Phase
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clickvis· Visual judgment- Work product
WP07· Simulation result- Conditions
licensed· Licensed pro app- Proposed difficulty
- 4 / 5
Proposed verifier
Hypothesis file has ≥4 features incl. D, A, R types; hits.csv ranked; enrichment factor at 5% ≥4 against hidden activity labels; hypothesis features match the five actives (fitness ≥1.5). The Schrödinger Python API and command-line utilities are absent from PATH, and job records detect any job not launched from a Maestro panel.
Proposed partial credit
35% valid hypothesis; 20% screen run; 45% enrichment (scaled from EF 1 to 4).
R08.05.01.03-T17 Set up an FEP+ perturbation map with required edges and a cycle closure
Original instruction
In Maestro open the FEP+ panel with input/series.maegz (8 congeneric ligands posed in the receptor). Build the perturbation map, edit it so it contains edges lig1–lig5 and a closed cycle lig3–lig6–lig7, remove any edge with similarity <0.5, and save the map as output/series.fmp without running it.
- Platforms
win· Windowsmac· macOSlin· Linux- Applications
- Schrödinger Maestro · FEP+
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgment- Work product
WP06· Code/engineering- Conditions
licensed· Licensed pro apptutorial· Follow docs/tutorial- Proposed difficulty
- 4 / 5
Proposed verifier
Parsing series.fmp: all 8 ligands connected; edges lig1–lig5, lig3–lig6, lig6–lig7, lig3–lig7 present; no edge with similarity <0.5; receptor included. No job launched (job DB empty). The Schrödinger Python API and command-line utilities are not available on PATH, and a file-system audit log flags a series.fmp not written by Maestro.
Proposed partial credit
25% map built; 25% lig1–lig5 edge; 30% cycle closure; 20% low-similarity edges removed.
R08.05.01.03-T18 Model a missing activation loop, cap termini and resolve altlocs in MOE
Original instruction
input/kinase.pdb lacks activation-loop residues 170–178 and has alternate locations. In MOE Structure Preparation keep the highest-occupancy altlocs, build the loop using input/template.pdb as template, cap chain termini with ACE/NME, and save output/kinase_prepped.pdb.
- Platforms
win· Windowsmac· macOS- Applications
- MOE
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & formsvis· Visual judgment- Work product
WP04· 3D/spatial model- Conditions
licensed· Licensed pro app- Proposed difficulty
- 3 / 5
Proposed verifier
Residues 170–178 present with correct sequence and loop Cα RMSD <2 Å to the template-based reference; no altlocs; ACE/NME caps at both termini; no chain breaks remain. The MOE SVL console and moebatch are disabled; preparation must run from the Structure Preparation panel.
Proposed partial credit
40% loop built; 20% altlocs; 20% caps; 20% no breaks.
R08.05.01.03-T19 Take a messy raw PDB from preparation through validated docking to an MD-ready system
Original instruction
input/raw_complex.pdb has altlocs, missing side chains, crystallization additives and the ligand as UNL without bond orders (true SMILES in input/ligand.smi). Prepare the protein, fix the ligand chemistry, validate by redocking (RMSD <2 Å), then build an Amber system (ff19SB, GAFF2/AM1-BCC, TIP3P, 0.15 M NaCl). Deliver output/redock.pdb, system.prmtop, system.inpcrd.
- Platforms
mac· macOSlin· Linuxwin· Windows- Applications
- UCSF ChimeraX · AutoDock Vina · AmberTools
- Interfaces
desk· Desktop GUIterm· Terminal- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clickcode· Code & commandsvis· Visual judgment- Work product
WP06· Code/engineering- Conditions
long· Long-horizonmultiapp· Multi-app- Proposed difficulty
- 5 / 5
Proposed verifier
Ligand in topology matches ligand.smi (InChIKey); additives removed; redock RMSD <2 Å; system: net charge 0, 0.15 M NaCl ±2 ions; 1,000-step sander minimization runs without error and energy decreases.
Proposed partial credit
25% protein and ligand prepared; 20% redock; 35% system build; 20% minimization runs.
R08.05.01.03-T20 Set up a 1 ns explicit-solvent NAMD simulation with VMD QwikMD
Original instruction
In VMD open QwikMD with input/protein.pdb: explicit solvent, 0.15 M NaCl, 310 K, protocol minimization → annealing → equilibration → 1 ns MD with 2 fs timestep. Prepare (do not run) the simulation into output/qwikmd/.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- VMD · QwikMD · NAMD
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & forms- Work product
WP06· Code/engineering- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
output/qwikmd/ holds PSF/PDB and NAMD config files: temperature 310, timestep 2.0, PME on, MD steps = 500,000; PSF ion count matches 0.15 M for the water count ±2; four protocol stages present. VMD's Tk/Tcl console and text-mode (-dispdev text -e) scripting are disabled; files must be generated by the QwikMD panel.
Proposed partial credit
25% system solvated/ionized; 30% protocol stages; 30% MD parameters; 15% files written.
Mapped research references
Existing benchmark-to-class links from the research catalog. They are not record-level annotations, executions or product endorsements.