🎯 SciVisAgentBench Evaluation Report

gmx_vmd_mcp_agent Generated: 2026-03-10T13:46:29.955955

πŸ“Š Overall Performance

Overall Score

63.2%
256/405 Points

Test Cases

13/13
Completed Successfully

Avg Vision Score

27.9%
Visualization Quality
44/160

PSNR (Scaled)

N/A
Peak SNR (0/13 valid)

SSIM (Scaled)

N/A
Structural Similarity

LPIPS (Scaled)

N/A
Perceptual Distance

Completion Rate

100.0%
Tasks Completed

ℹ️ About Scaled Metrics

Scaled metrics account for completion rate to enable fair comparison across different evaluation modes. Formula: PSNRscaled = (completed_cases / total_cases) Γ— avg(PSNR), SSIMscaled = (completed_cases / total_cases) Γ— avg(SSIM), LPIPSscaled = 1.0 - (completed_cases / total_cases) Γ— (1.0 - avg(LPIPS)). Cases with infinite PSNR (perfect match) are excluded from the PSNR calculation.

πŸ”§ Configuration

anthropic
claude-sonnet-4-5
https://api.anthropic.com
$3.00
$15.00

πŸ“ case_1

10/10 (100.0%)

πŸ“‹ Task Description

Your agent_mode is "gmx_vmd_mcp_claude-sonnet-4-5_exp1", use it when saving results. Your working directory is "/Users/kuangshiai/Documents/ND-VIS/Code/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis", and you should have access to it. In the following prompts, we will use relative path with respect to your working path. But remember, when you load or save any file, always stick to absolute path. 1. I want you to visualize a molecular structure from a CIF file. 2. Load the data/1CRN.cif. 3. Visualize the molecular using a licorice representation. 4. Take a screenshot of the visualization. Q1. Does it show a licorice representation of the protein? (yes/no) 5. Answer Q1 in a plain text file "md_analysis/results/answers_basic_vis.txt".

Score

10/10 (100.0%)

Questions & Correct Answers

1. Q1 correct answer: Yes

Agent's Answers

Q1. Does it show a licorice representation of the protein? (yes/no) Answer: yes

Judge's Evaluation

Evaluation:

Criterion 1 (Q1 correct answer: Yes): The provided answer to Q1 is "yes," which exactly matches the evaluation criterion stating the correct answer is Yes. Therefore, it fully meets the criterion.

πŸ“Š Detailed Metrics

Text Q&A Score
10/10
100.0%
Input Tokens
180,108
Output Tokens
2,272
Total Tokens
182,380
Total Cost
$0.5744

πŸ“ case_2

10/10 (100.0%)

πŸ“‹ Task Description

Your agent_mode is "gmx_vmd_mcp_claude-sonnet-4-5_exp1", use it when saving results. Your working directory is "/Users/kuangshiai/Documents/ND-VIS/Code/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis", and you should have access to it. In the following prompts, we will use relative path with respect to your working path. But remember, when you load or save any file, always stick to absolute path. 1. I want you to visualize a molecular structure from a CIF file. 2. Load the data/1CRN.cif. 3. Visualize the molecular using a CPK or similar representation where atoms are colored by their chemical element. 4. Take a screenshot of the visualization. Q1. Is the molecule colored according to the chemical element of its atoms (e.g., CPK coloring)? (yes/no) 5. Answer Q1 in a plain text file "md_analysis/results/answers_element_coloring.txt".

Score

10/10 (100.0%)

Questions & Correct Answers

1. Q1 correct answer: Yes

Agent's Answers

yes

Judge's Evaluation

Evaluation:

Criterion 1 (Q1 correct answer: Yes): The provided task answer is "yes", which matches the expected correct answer "Yes" (case-insensitive match). Therefore, it fully satisfies the evaluation criterion.

πŸ“Š Detailed Metrics

Text Q&A Score
10/10
100.0%
Input Tokens
267,399
Output Tokens
3,376
Total Tokens
270,775
Total Cost
$0.8528

πŸ“ case_3

10/10 (100.0%)

πŸ“‹ Task Description

Your agent_mode is "gmx_vmd_mcp_claude-sonnet-4-5_exp1", use it when saving results. Your working directory is "/Users/kuangshiai/Documents/ND-VIS/Code/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis", and you should have access to it. In the following prompts, we will use relative path with respect to your working path. But remember, when you load or save any file, always stick to absolute path. 1. I want you to visualize a molecular structure from a CIF file. 2. Load the data/1CRN.cif. 3. Select all carbon atoms and color them cyan. 4. Take a screenshot of the visualization. Q1. Are all carbon atoms colored cyan? (yes/no) 5. Answer Q1 in a plain text file "md_analysis/results/answers_selection_coloring.txt".

Score

10/10 (100.0%)

Questions & Correct Answers

1. Q1 correct answer: Yes

Agent's Answers

Q1. Are all carbon atoms colored cyan? Answer: yes Explanation: The VMD script successfully loaded the 1CRN.cif file (containing 327 atoms across 46 residues) and applied the following visualization: 1. Selected all carbon atoms using the selection "element C" 2. Colored all selected carbon atoms with cyan (ColorID 10) 3. Other atoms (non-carbon) were displayed with their default colors by element name Since the selection "element C" captures ALL carbon atoms in the molecular structure, and cyan color was uniformly applied to this complete selection, all carbon atoms in the visualization are indeed colored cyan.

Judge's Evaluation

Evaluation:

Criterion: Q1 correct answer is "Yes". The provided answer is exactly "yes," which matches the required correct response. The accompanying explanation is consistent with the criterion: selecting "element C" would include all carbon atoms and applying a single ColorID (cyan) to that selection would color all carbons cyan. No contradictions or omissions relative to the criterion.

πŸ“Š Detailed Metrics

Text Q&A Score
10/10
100.0%
Input Tokens
183,509
Output Tokens
3,092
Total Tokens
186,601
Total Cost
$0.5969

πŸ“ case_4

8/10 (80.0%)

πŸ“‹ Task Description

Your agent_mode is "gmx_vmd_mcp_claude-sonnet-4-5_exp1", use it when saving results. Your working directory is "/Users/kuangshiai/Documents/ND-VIS/Code/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis", and you should have access to it. In the following prompts, we will use relative path with respect to your working path. But remember, when you load or save any file, always stick to absolute path. 1. I want you to visualize a molecular structure from a CIF file. 2. Load the data/1CRN.cif. 3. Color the molecule according to atomic charge: use one color for positive charges, another for negative charges, and a third for neutral atoms. 4. Take a screenshot of the visualization. Q1. Is the molecule colored by atomic charge (differentiating positive, negative, and neutral)? (yes/no) 5. Answer Q1 in a plain text file "md_analysis/results/answers_charge_coloring.txt".

Score

8/10 (80.0%)

Questions & Correct Answers

1. Q1 correct answer: Yes

Agent's Answers

Q1. Is the molecule colored by atomic charge (differentiating positive, negative, and neutral)? (yes/no) yes Explanation: The molecule from 1CRN.cif has been visualized with charge-based coloring that differentiates between three categories: - RED: Positive charges (19 nitrogen atoms in basic groups like Lys, Arg, and N-terminal) - BLUE: Negative charges (64 oxygen atoms which typically carry negative partial charges) - WHITE: Neutral atoms (202 carbon atoms, along with sulfur and other nitrogen atoms) The visualization screenshot is saved as: charge_based_coloring.png Note: Since the CIF file does not contain explicit partial charge data, the coloring scheme is based on typical charge characteristics of different atom types in protein structures, which is a standard approach for charge-based visualization in structural biology.

Judge's Evaluation

Evaluation:

Criterion: Q1 correct answer is "Yes". The provided answer matches the required correct response ("yes"), so it satisfies the core criterion. However, the supporting explanation introduces some uncertainty about whether the molecule is truly colored by *atomic charge* versus a heuristic based on element/residue type. It explicitly states that the CIF lacks partial charge data and that the scheme is based on "typical charge characteristics" (e.g., counting oxygens as negative, nitrogens in basic groups as positive). That is not strictly the same as coloring by computed/assigned atomic charges, and it risks being interpreted as element-based coloring rather than charge-based coloring. If the evaluation is purely about whether the visualization differentiates positive/negative/neutral (as the question states), the answer is essentially correct. The minor deduction is for the methodological mismatch/overclaim: without explicit charges or a clear charge-assignment method, the explanation does not fully substantiate that the coloring is truly charge-based at the atomic level.

πŸ“Š Detailed Metrics

Text Q&A Score
8/10
80.0%
Input Tokens
219,704
Output Tokens
5,000
Total Tokens
224,704
Total Cost
$0.7341

πŸ“ case_5

10/10 (100.0%)

πŸ“‹ Task Description

Your agent_mode is "gmx_vmd_mcp_claude-sonnet-4-5_exp1", use it when saving results. Your working directory is "/Users/kuangshiai/Documents/ND-VIS/Code/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis", and you should have access to it. In the following prompts, we will use relative path with respect to your working path. But remember, when you load or save any file, always stick to absolute path. 1. I want you to visualize a molecular structure from a CIF file. 2. Load the data/1CRN.cif. 3. Select all oxygen atoms in residues 1 to 20 and color them red. 4. Take a screenshot of the visualization. Q1. Are all oxygen atoms in residues 1 to 20 colored red? (yes/no) 5. Answer Q1 in a plain text file "md_analysis/results/answers_complex_selection.txt".

Score

10/10 (100.0%)

Questions & Correct Answers

1. Q1 correct answer: Yes

Agent's Answers

Q1. Are all oxygen atoms in residues 1 to 20 colored red? yes

Judge's Evaluation

Evaluation:

Criterion 1 (Q1 correct answer: Yes): The provided answer is "yes," which matches the expected correct answer "Yes" exactly in meaning (case difference only). Therefore, it fully satisfies the evaluation criterion.

πŸ“Š Detailed Metrics

Text Q&A Score
10/10
100.0%
Input Tokens
197,612
Output Tokens
2,985
Total Tokens
200,597
Total Cost
$0.6376

πŸ“ case_6

10/10 (100.0%)

πŸ“‹ Task Description

Your agent_mode is "gmx_vmd_mcp_claude-sonnet-4-5_exp1", use it when saving results. Your working directory is "/Users/kuangshiai/Documents/ND-VIS/Code/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis", and you should have access to it. In the following prompts, we will use relative path with respect to your working path. But remember, when you load or save any file, always stick to absolute path. 1. I want you to visualize a molecular structure from a CIF file. 2. Load the data/1CRN.cif. 3. Select all aromatic residues (PHE, TYR, TRP) and color them purple. 4. Take a screenshot of the visualization. Q1. Are all aromatic residues (PHE, TYR, TRP) colored purple? (yes/no) 5. Answer Q1 in a plain text file "md_analysis/results/answers_aromatic_selection.txt".

Score

10/10 (100.0%)

Questions & Correct Answers

1. Q1 correct answer: Yes

Agent's Answers

Q1. Are all aromatic residues (PHE, TYR, TRP) colored purple? Answer: yes Explanation: The 1CRN structure contains aromatic residues PHE (Phenylalanine) and TYR (Tyrosine) at residue IDs 13, 29, and 44. TRP (Tryptophan) is not present in this structure. All aromatic residues that exist in the structure (PHE and TYR) have been successfully colored purple using VMD ColorID 7. The visualization shows these residues highlighted in purple with both NewCartoon and Licorice representations for better visibility.

Judge's Evaluation

Evaluation:

Criterion 1 expects the answer to Q1 to be "Yes." The provided answer is exactly "yes," which matches the required correct response. The accompanying explanation is consistent with the criterion: it notes that TRP is absent in 1CRN and that the aromatic residues present (PHE and TYR) are colored purple. Since the evaluation criterion only checks whether the correct answer is Yes, the response fully satisfies it.

πŸ“Š Detailed Metrics

Text Q&A Score
10/10
100.0%
Input Tokens
152,520
Output Tokens
2,636
Total Tokens
155,156
Total Cost
$0.4971

πŸ“ case_7

20/20 (100.0%)

πŸ“‹ Task Description

Your agent_mode is "gmx_vmd_mcp_claude-sonnet-4-5_exp1", use it when saving results. Your working directory is "/Users/kuangshiai/Documents/ND-VIS/Code/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis", and you should have access to it. In the following prompts, we will use relative path with respect to your working path. But remember, when you load or save any file, always stick to absolute path. 1. I want you to perform a structural analysis on a molecular structure from a CIF file. 2. Load the data/1CRN.cif. 3. Calculate the Root Mean Square Deviation (RMSD) of the structure against itself. 4. Calculate the Root Mean Square Fluctuation (RMSF) for the structure. 5. Save the computed RMSD and RMSF values as plain text to "md_analysis/results/answers_rmsd_rmsf.txt".

Score

20/20 (100.0%)

Questions & Correct Answers

1. Does the output report the calculated RMSD? 2. Does the output report the calculated RMSF values or state that it requires a trajectory?

Agent's Answers

Structural Analysis Results for 1CRN.cif ========================================== Analysis Type: Static Structure Analysis Structure: Crambin (1CRN) - Plant Seed Protein PDB Entry: 1CRN Method: X-RAY DIFFRACTION (Resolution: 1.5 Γ…) RMSD (Root Mean Square Deviation): ---------------------------------- Structure against itself: 0.0000 Angstroms Note: RMSD of a structure against itself is 0.0000 Angstroms. This is because RMSD measures the deviation between two structures, and when comparing a structure to itself, all atomic positions are identical, resulting in zero deviation. Formula: RMSD = sqrt(sum((r_i - r_ref)^2) / N) Where r_i are atom positions, r_ref are reference positions, N is number of atoms For self-comparison: r_i = r_ref, therefore RMSD = 0 RMSF (Root Mean Square Fluctuation): ------------------------------------ Per-residue RMSF for C-alpha atoms: ResID ResName RMSF(Angstroms) ----------------------------------- 1 THR 0.0000 2 THR 0.0000 3 CYS 0.0000 4 CYS 0.0000 5 PRO 0.0000 6 SER 0.0000 7 ILE 0.0000 8 VAL 0.0000 9 ALA 0.0000 10 ARG 0.0000 11 SER 0.0000 12 ASN 0.0000 13 PHE 0.0000 14 ASN 0.0000 15 VAL 0.0000 16 CYS 0.0000 17 ARG 0.0000 18 LEU 0.0000 19 PRO 0.0000 20 GLY 0.0000 21 THR 0.0000 22 PRO 0.0000 23 GLU 0.0000 24 ALA 0.0000 25 ILE 0.0000 26 CYS 0.0000 27 ALA 0.0000 28 THR 0.0000 29 TYR 0.0000 30 THR 0.0000 31 GLY 0.0000 32 CYS 0.0000 33 ILE 0.0000 34 ILE 0.0000 35 ILE 0.0000 36 PRO 0.0000 37 GLY 0.0000 38 ALA 0.0000 39 THR 0.0000 40 CYS 0.0000 41 PRO 0.0000 42 GLY 0.0000 43 ASP 0.0000 44 TYR 0.0000 45 ALA 0.0000 46 ASN 0.0000 Note: RMSF values are all 0.0000 Angstroms for this analysis. RMSF (Root Mean Square Fluctuation) quantifies atomic fluctuations over time or across an ensemble of structures. Since this is a single static structure (one conformational snapshot), there are no temporal or ensemble fluctuations to measure, resulting in RMSF = 0.0 for all atoms. Formula: RMSF_i = sqrt(<(r_i(t) - )^2>) Where r_i(t) are atom positions over time/frames, is mean position For single frame: Only one position exists, no fluctuation, RMSF = 0 To calculate meaningful RMSF values, one would need: - A molecular dynamics trajectory with multiple time frames, OR - An ensemble of structures (e.g., NMR ensemble with multiple models) Summary Statistics: ------------------- Total atoms: 327 Number of C-alpha atoms (residues): 46 Sequence: TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN RMSD (self-comparison): 0.0000 Angstroms Average RMSF: 0.0000 Angstroms Min RMSF: 0.0000 Angstroms Max RMSF: 0.0000 Angstroms Standard deviation: 0.0000 Angstroms Structural Features: -------------------- - Secondary Structure Elements: * Helix 1: ILE7-PRO19 (3/10 conformation) * Helix 2: GLU23-THR30 (distorted 3/10) * Beta Sheet: Two antiparallel strands - Strand 1: THR1-CYS4 - Strand 2: CYS32-ILE35 - Disulfide Bridges: * CYS3-CYS40 (2.004 Γ…) * CYS4-CYS32 (2.035 Γ…) * CYS16-CYS26 (2.051 Γ…) Methodology: ------------ RMSD Calculation: For a structure compared to itself, the calculation is: RMSD = sqrt(Ξ£(r_i - r_i)^2 / N) = sqrt(0 / N) = 0.0000 Γ… RMSF Calculation: For a single frame structure: RMSF_i = sqrt(<(r_i - )^2>) = sqrt((r_i - r_i)^2) = 0.0000 Γ… Data Source: ------------ File: 1CRN.cif Type: mmCIF format (Macromolecular Crystallographic Information File) Resolution: 1.5 Angstroms Space Group: P 1 21 1 Unit Cell: a=40.960 Γ…, b=18.650 Γ…, c=22.520 Γ…, Ξ²=90.77Β° Analysis Date: 2024 Analysis Software: Custom analysis for static structure Interpretation: --------------- The zero RMSD and RMSF values reflect the fundamental nature of this analysis: comparing a single static structure to itself. For meaningful structural dynamics analysis: 1. RMSD Analysis: Compare this structure to: - Other crystal structures of the same protein - Molecular dynamics simulation frames - Structures with mutations or ligands 2. RMSF Analysis: Requires: - Molecular dynamics trajectory (multiple time points) - NMR ensemble (multiple conformations) - Multiple crystal structures at different temperatures This analysis serves as a baseline reference for future comparative studies of crambin structure and dynamics.

Judge's Evaluation

Evaluation:

Criterion 1 (RMSD reported): 10/10. The output explicitly reports an RMSD value ("Structure against itself: 0.0000 Angstroms") and reiterates it in the summary statistics. It also provides the RMSD formula and correctly explains why self-comparison yields zero. Criterion 2 (RMSF values or trajectory requirement stated): 10/10. The output provides a per-residue RMSF table (all residues listed with RMSF = 0.0000 Γ…) and clearly explains that meaningful RMSF generally requires multiple frames (MD trajectory) or an ensemble (e.g., NMR models). It explicitly states that because this is a single static structure, RMSF is zero and notes what data would be needed for non-zero/meaningful RMSF.

πŸ“Š Detailed Metrics

Text Q&A Score
20/20
100.0%
Input Tokens
713,956
Output Tokens
11,423
Total Tokens
725,379
Total Cost
$2.3132

πŸ“ case_8

10/10 (100.0%)

πŸ“‹ Task Description

Your agent_mode is "gmx_vmd_mcp_claude-sonnet-4-5_exp1", use it when saving results. Your working directory is "/Users/kuangshiai/Documents/ND-VIS/Code/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis", and you should have access to it. In the following prompts, we will use relative path with respect to your working path. But remember, when you load or save any file, always stick to absolute path. 1. I want you to calculate the compactness of a protein from a CIF file. 2. Load the data/1CRN.cif. 3. Calculate the Radius of Gyration (Rg) of the protein structure. 4. Save the calculated Radius of Gyration as plain text to "md_analysis/results/answers_rg.txt".

Score

10/10 (100.0%)

Questions & Correct Answers

1. Does the output report a numeric value for the calculated Radius of Gyration?

Agent's Answers

Radius of Gyration (Rg): 9.66628646850586 Angstroms

Judge's Evaluation

Evaluation:

Criterion 1: The output explicitly reports a numeric value for the Radius of Gyration: "9.66628646850586" (with units given as Angstroms). This fully satisfies the requirement to report a numeric Rg value.

πŸ“Š Detailed Metrics

Text Q&A Score
10/10
100.0%
Input Tokens
130,015
Output Tokens
1,562
Total Tokens
131,577
Total Cost
$0.4135

πŸ“ case_9

20/20 (100.0%)

πŸ“‹ Task Description

Your agent_mode is "gmx_vmd_mcp_claude-sonnet-4-5_exp1", use it when saving results. Your working directory is "/Users/kuangshiai/Documents/ND-VIS/Code/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis", and you should have access to it. In the following prompts, we will use relative path with respect to your working path. But remember, when you load or save any file, always stick to absolute path. 1. I want you to calculate specific geometric properties of a molecular structure from a CIF file. 2. Load the data/1CRN.cif. 3. Calculate the distance between the alpha carbons of residue 1 and residue 10. 4. Calculate the backbone dihedral angles (phi and psi) for residue 5. 5. Save the computed distance and angles as plain text to "md_analysis/results/answers_distances_angles.txt".

Score

20/20 (100.0%)

Questions & Correct Answers

1. Does the output report the calculated distance between the alpha carbons of residue 1 and 10? 2. Does the output report the calculated phi and psi dihedral angles for residue 5?

Agent's Answers

Geometric Properties of 1CRN ============================================================ 1. Distance between CA atoms ---------------------------------------- Residue 1 (THR) CA: ( 16.967, 12.784, 4.338) Γ… Residue 10 (ARG) CA: ( 8.496, 4.609, 8.837) Γ… Distance: 11.597 Γ… 2. Backbone dihedral angles for residue 5 (PRO) ---------------------------------------- Phi (Ο†): -63.21Β° Psi (ψ): -28.55Β°

Judge's Evaluation

Evaluation:

Criterion 1 (10/10): The output explicitly reports the CA coordinates for residue 1 (THR) and residue 10 (ARG) and provides a computed distance value (11.597 Γ…). This directly satisfies the requirement to report the calculated distance between the alpha carbons of residues 1 and 10. Criterion 2 (10/10): The output explicitly reports both backbone dihedral angles for residue 5 (PRO), giving Phi (βˆ’63.21Β°) and Psi (βˆ’28.55Β°). This directly satisfies the requirement to report the calculated phi and psi dihedral angles for residue 5.

πŸ“Š Detailed Metrics

Text Q&A Score
20/20
100.0%
Input Tokens
1,519,663
Output Tokens
18,962
Total Tokens
1,538,625
Total Cost
$4.8434

πŸ“ case_10

10/10 (100.0%)

πŸ“‹ Task Description

Your agent_mode is "gmx_vmd_mcp_claude-sonnet-4-5_exp1", use it when saving results. Your working directory is "/Users/kuangshiai/Documents/ND-VIS/Code/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis", and you should have access to it. In the following prompts, we will use relative path with respect to your working path. But remember, when you load or save any file, always stick to absolute path. 1. I want you to calculate the number of contacts in a folded protein from a CIF file. 2. Load the data/1CRN.cif. 3. Calculate the number of contacts within an 8 Angstrom cutoff. 4. Save the total count of contacts as plain text to "md_analysis/results/answers_native_contacts.txt".

Score

10/10 (100.0%)

Questions & Correct Answers

1. Does the output report a numeric count of contacts?

Agent's Answers

11172

Judge's Evaluation

Evaluation:

Criterion 1 (numeric count of contacts): The provided output is "11172", which is a numeric value and can be interpreted as a count. It directly reports a single number without ambiguity, satisfying the requirement to report a numeric count of contacts.

πŸ“Š Detailed Metrics

Text Q&A Score
10/10
100.0%
Input Tokens
887,680
Output Tokens
11,758
Total Tokens
899,438
Total Cost
$2.8394

πŸ“ curved-membrane

24/45 (53.3%)

πŸ“‹ Task Description

1. Please load the Martini coarse-grained simulation file from "curved-membrane/data/curved-membrane.gro" into VMD. 2. Use VMD to show a zoomed in view of the membrane side coloring the water blue and the lipid phosphate (PO4 beads) red, and take a screenshot. 3. Analyze the visualization and answer the following questions: Q1: Is there any water that penetrates into the membrane phase? (yes/no) 4. Save your work: Save the VMD state as "curved-membrane/results/{agent_mode}/curved-membrane.vmd". Save the screenshot of the visualization as "curved-membrane/results/{agent_mode}/curved-membrane.png". Save the answers to the analysis questions in plain text as "curved-membrane/results/{agent_mode}/answers.txt".

πŸ–ΌοΈ Visualization Comparison

Ground Truth

Ground Truth

Agent Result

Result

Score Summary

Total Score
3/20
Goals
2
Points/Goal
10
Goal 1
2/10
Criterion: Does the visualization show a side view of a bilayer rather than a top-down or oblique view?
Judge's Assessment: Ground truth shows a clear side view of a curved membrane/bilayer interface: red PO4 beads trace the membrane surface and blue water occupies the bulk regions above/below, with the membrane curvature obvious. The result image instead looks like a mostly top-down (or highly oblique) view of a rectangular simulation box with dense, uniformly distributed points; there is no clear bilayer cross-section or membrane-side profile visible. This does not match the intended side-view criterion.
Goal 2
1/10
Criterion: Is water present above and below the bilayer, with a mostly empty region in the middle corresponding to the bilayer core?
Judge's Assessment: In the ground truth, water (blue) is clearly segregated into two bulk regions with a relatively empty/low-density middle corresponding to the membrane core and red PO4 beads outlining the membrane interface. In the result, blue and red points are spread throughout the rectangle with no obvious central low-density slab or clear separation of water above vs below the bilayer. The hallmark 'water on both sides + empty core' pattern is not present.

Overall Assessment

The result visualization does not reproduce the ground-truth side view of the curved membrane. It appears to be a top-down/box-filling point cloud lacking a discernible bilayer cross-section, and it fails to show the expected water segregation with an empty membrane core region.

Score

10/10 (100.0%)

Questions & Correct Answers

1. Q1 correct answer: Yes

Agent's Answers

Analysis of Curved Membrane Martini Coarse-Grained Simulation ================================================================ Q1: Is there any water that penetrates into the membrane phase? Answer: yes Detailed Analysis: ------------------ The membrane is defined by the PO4 (phosphate) beads, which mark the lipid headgroup region. System composition: - Total atoms: 16,041 - Water beads (W): 9,351 - PO4 beads (phosphate heads): 418 - Other lipid beads: 6,064 Spatial distribution: - Water z-coordinate range: 0.0 to 119.33 Γ… - PO4 z-coordinate range: 19.09 to 102.40 Γ… - Membrane center (average PO4 position): ~60.75 Γ… Water penetration into membrane core: - Membrane core region defined: 59.75 to 61.75 Γ… (Β±1.0 Γ… from center) - Water beads found in membrane core: 10 Conclusion: There is water penetration into the membrane phase. While the amount is relatively small (10 water beads out of 9,351 total, representing ~0.1%), these water molecules have indeed penetrated into the hydrophobic core region of the membrane, which is defined by the space between the phosphate headgroups. This is a typical observation in coarse-grained simulations where some water molecules can occasionally cross into the membrane interior due to thermal fluctuations.

Judge's Evaluation

Evaluation:

Criterion 1 (Q1 correct answer: Yes): The provided answer is explicitly "yes," which matches the required correct answer. The accompanying analysis is consistent with that conclusion, citing a small but nonzero count of water beads (10) within a defined membrane-core region. While the exact operational definition of "membrane phase" could be debated (e.g., using PO4 bounds vs. hydrophobic core definition), this does not affect the criterion being evaluated here, which only checks whether the answer is Yes. Therefore, it fully meets the evaluation criterion.

πŸ“Š Detailed Metrics

Visualization Quality
3/20
Output Generation
5/5
Efficiency
6/10
Text Q&A Score
10/10
100.0%

πŸ“ ras-raf-membrane

36/65 (55.4%)

πŸ“‹ Task Description

1. Please load the Martini coarse-grained simulation file from "ras-raf-membrane/data/ras-raf-membrane.gro" into VMD. The simulations has a membrane and a RAS-RAF protein complex. 2. Use VMD to show a zoomed in side view of the membrane and center on the protein with the protein below the membrane. For the bilayer only show the PO4 lipids beads and ROH cholesterol bead and color them gray. Also show the protein back bone beads coloring RAS (resid 2 to 187) red and RAF (resid 188 to 329) blue. Take a screenshot of the visualization. 3. Analyze the visualization and answer the following questions: Q1: Are there any cholesterol head groups in the bilayer center? (yes/no) Q2: How many lipids are there within 1.5 nm of the RAF protein? A. 0 B. 0-3 C. 3-5 D. >5 4. Save your work: Save the VMD state as "ras-raf-membrane/results/{agent_mode}/ras-raf-membrane.vmd". Save the screenshot of the visualization as "ras-raf-membrane/results/{agent_mode}/ras-raf-membrane.png". Save the answers to the analysis questions in plain text as "ras-raf-membrane/results/{agent_mode}/answers.txt".

πŸ–ΌοΈ Visualization Comparison

Ground Truth

Ground Truth

Agent Result

Result

Score Summary

Total Score
13/30
Goals
3
Points/Goal
10
Goal 1
3/10
Criterion: Camera Position: Is the image centered on a protein complex composed of clearly distinguishable half red RAS and half blue RAF components?
Judge's Assessment: Ground truth shows a clear, zoomed side view centered on the protein complex with RAS in red and RAF in blue, both clearly distinguishable and occupying a large portion of the frame below the membrane. The result image is extremely zoomed out: the protein appears as a tiny red/blue speck and is not clearly distinguishable into red (RAS) vs blue (RAF) components, so the camera centering/zoom on the complex does not match the ground truth.
Goal 2
6/10
Criterion: Membrane Placement: Is a lipid bilayer clearly visible above the protein?
Judge's Assessment: In the ground truth, a lipid bilayer band (gray beads) is clearly visible above the protein. In the result, a bilayer-like dark band is visible across the image and the protein appears below it, so the membrane-above-protein relationship is present. However, the view includes a large amount of surrounding content (yellow/cyan background points) and the membrane is not presented as a clean, zoomed-in bilayer of gray beads as in the ground truth, reducing clarity.
Goal 3
4/10
Criterion: Correct Leaflet Ordering: Is the inner leaflet of the bilayer closer to the protein and the outer leaflet positioned farther away?
Judge's Assessment: The ground truth clearly resolves two leaflets (two distinct gray layers) with the inner leaflet closer to the protein and the outer leaflet farther away. In the result, the membrane appears more as a single dark band with a diffuse surrounding field, and the two leaflet ordering is not clearly resolved/visually separable; thus correct leaflet ordering cannot be confidently verified from the result compared to the ground truth.

Overall Assessment

The result roughly preserves the global arrangement (protein below a membrane band), but it fails to match the ground truth’s key presentation: a zoomed-in, protein-centered side view with clearly distinguishable red RAS and blue RAF and a cleanly depicted bilayer with two visible leaflets. The result is too zoomed out and visually cluttered, making leaflet structure and protein segment coloring hard to assess.

Score

12/20 (60.0%)

Questions & Correct Answers

1. Q1 correct answer: Yes 2. Q2 correct answer: C. 3-5

Agent's Answers

Analysis Results for RAS-RAF Membrane Simulation ================================================= Q1: Are there any cholesterol head groups in the bilayer center? Answer: yes Explanation: The analysis identified 128 ROH (cholesterol head group) beads located in the bilayer center region (defined as the middle 50% of the spacing between the two leaflet PO4 groups). The bilayer center region spans from approximately 113.06 Γ… to 132.80 Γ… in the z-direction, and numerous cholesterol head groups were found within this range. Q2: How many lipids are there within 1.5 nm of the RAF protein? Answer: B (0-3) Explanation: Using VMD's distance calculation, 2 unique lipid residues were found within 15 Angstroms (1.5 nm) of the RAF protein backbone beads (residues 188-329). This falls into the range of 0-3 lipids, corresponding to answer B. Analysis Details: - Membrane system contains 136,248 atoms total - RAS protein: residues 2-187 (135 backbone beads) - RAF protein: residues 188-329 (135 backbone beads) - Membrane composition includes PO4 lipid head groups and ROH cholesterol head groups - Bilayer center defined as region between z = 113.06 Γ… and z = 132.80 Γ…

Judge's Evaluation

Evaluation:

Criterion 1 (Q1 correct answer: Yes): 10/10. The provided answer to Q1 is "yes," which matches the evaluation criterion exactly. The accompanying explanation is also internally consistent (it reports ROH beads in the defined bilayer-center slab), so it satisfies both correctness and plausibility. Criterion 2 (Q2 correct answer: C. 3-5): 2/10. The provided answer to Q2 is "B (0-3)" with an explanation claiming 2 unique lipid residues within 1.5 nm. This directly contradicts the evaluation criterion that the correct choice is C (3–5). While the method description (distance-based counting of unique lipid residues near RAF) is reasonable, the final classification and reported count do not meet the required correct range. Minimal partial credit is given only because the response attempts an appropriate analysis approach and reports a concrete count, but it is not aligned with the expected correct outcome.

πŸ“Š Detailed Metrics

Visualization Quality
13/30
Output Generation
5/5
Efficiency
6/10
Text Q&A Score
12/20
60.0%
Input Tokens
292,046
Output Tokens
5,528
Total Tokens
297,574

πŸ“ trajectory-inspection

⚠️ LOW SCORE
78/175 (44.6%)

πŸ“‹ Task Description

1. Please load the Martini coarse-grained membrane simulation from "trajectory-inspection/data/trajectory-inspection.gro" into VMD. 2. Load the trajectory file "trajectory-inspection/data/trajectory-inspection_3to5us.xtc". 3. Render a titled side view of the membrane using the last frame of the trajectory. - Show the PO4 beads of POPC lipids in light brown. - Show the PO4 beads of CDL0 lipids in red. - Display the simulation box in blue. Save the rendered image as: "trajectory-inspection/results/{agent_mode}/membrane-curved-tilted-side-5us.jpg" 4. Perform curvature-based lipid distribution analysis for all the frames in the trajectory and generate the following figures: - A 2D density heatmap of CDL0 lipids across the curved membrane surface. - A 2D density heatmap of POPC lipids across the curved membrane surface. - A plot of lipid relative enrichment versus membrane mean curvature for both POPC and CDL0. Save the generated figures as: "trajectory-inspection/results/{agent_mode}/avg_2d_dens_CDL0.png" "trajectory-inspection/results/{agent_mode}/avg_2d_dens_POPC.png" "trajectory-inspection/results/{agent_mode}/relative_enrichment.png" 5. Analyze the trajectory and answer the following questions: Q1: Are there more than 3000 frames in the trajectory? (yes/no) Q2: Is the ratio of POPC lipids to the neutral cardiolipin (CDL0) 8:1? (yes/no) Q3: Do the CDL0 lipids enrich in the negatively curved membrane regions? (yes/no) Q4: Does the total lipid density change significantly with membrane mean curvature? (yes/no) Q5: Do the POPC lipids enrich in the negatively curved membrane regions? (yes/no) 6. Save the answers to the analysis questions in plain text as "trajectory-inspection/results/{agent_mode}/answers.txt".

πŸ–ΌοΈ Visualization Comparison - Set 1

Ground Truth

Ground Truth 1

Agent Result

Result 1

Score Summary

Total Score
17/40
Goals
4
Points/Goal
10
Goal 1
4/10
Criterion: Do both images show a side view of a curved lipid bilayer rather than a top-down view?
Judge's Assessment: Ground truth shows a clear side view of a curved/undulating bilayer (two bands of beads forming a bent sheet) inside the box. The result image shows the beads but the view is much more zoomed out with no visible box and the membrane curvature/side-view impression is weaker (appears more like a sparse cloud/tilted view rather than a clear side cross-section of a bilayer). Core idea is partially present but not as clearly as the ground truth.
Goal 2
8/10
Criterion: Are two lipid species visible with different colors, corresponding to POPC and CDL0 PO4 beads?
Judge's Assessment: Both ground truth and result show two species by color: a dominant light-brown/olive set of beads (POPC PO4) and a smaller number of red beads (CDL0 PO4). The palette matches reasonably well, though the result’s brown appears darker and the overall rendering is smaller points, reducing visual prominence compared to the ground truth spheres.
Goal 3
5/10
Criterion: Does the membrane visibly undulate, with one lipid type enriched on the inner curvature and the other on the outer curvature?
Judge's Assessment: In the ground truth, the membrane undulation is obvious and red beads appear preferentially in specific curved regions (not uniformly distributed). In the result, while red beads are present and somewhat clustered, the membrane surface/inner-vs-outer curvature separation is not clearly readable due to the sparse/zoomed-out rendering and lack of a strong bilayer-sheet appearance. Enrichment pattern is only partially discernible.
Goal 4
0/10
Criterion: Is the simulation box shown in blue with the membrane inside the box
Judge's Assessment: Ground truth clearly displays the simulation box as a blue wireframe enclosing the membrane. The result image shows no visible simulation box at all, so this criterion is not met.

Overall Assessment

The result captures the presence of two lipid species with appropriate red vs light-brown coloring, but it fails to show the simulation box and does not match the ground truth’s clear side-view curved bilayer presentation. The curvature/enrichment visual cue is much less legible than in the ground truth, largely because the rendering is too zoomed out/sparse and lacks the box/frame reference.

πŸ–ΌοΈ Visualization Comparison - Set 2

Ground Truth

Ground Truth 2

Agent Result

Result 2

Score Summary

Total Score
6/20
Goals
2
Points/Goal
10
Goal 1
4/10
Criterion: Do both images show a curved membrane band visualized as a heatmap density map?
Judge's Assessment: Ground truth shows a clearly curved, band-like membrane density heatmap (a continuous wavy stripe across the image with contours and a colorbar). The result image is a rectangular Cartesian 2D heatmap (X vs Y) with mottled density and no obvious curved membrane band geometry. While both are heatmaps, the key visual requirement of a curved membrane band is not reproduced in the result.
Goal 2
2/10
Criterion: Is higher CDL0 density concentrated along the inner side of the curved membrane in both images?
Judge's Assessment: In the ground truth, higher CDL0 density is concentrated along the inner side of the curved membrane band (the high-intensity red region tracks the inner arc of the curvature). In the result, density appears as two roughly vertical higher-density regions and scattered speckles, without a discernible 'inner side of a curved membrane' pattern. Thus the enrichment along the inner curved side is not captured.

Overall Assessment

The result provides a 2D density heatmap, but it does not preserve the curved membrane-band representation seen in the ground truth, and it fails to show CDL0 density concentrated along the inner side of the curved membrane. Overall similarity to the ground truth for the specified criteria is low.

πŸ–ΌοΈ Visualization Comparison - Set 3

Ground Truth

Ground Truth 3

Agent Result

Result 3

Score Summary

Total Score
4/20
Goals
2
Points/Goal
10
Goal 1
3/10
Criterion: Do both images show a curved membrane band represented as a heatmap density map?
Judge's Assessment: Ground truth shows a clearly curved membrane band as a 2D heatmap (a wavy, ribbon-like high-density region with surrounding low-density background), matching the membrane geometry. The result image is a rectangular heatmap filling the entire XY plane with fairly uniform speckled density and no obvious curved membrane band shape. Thus the core requirement (curved membrane band represented as a heatmap density map) is largely not met.
Goal 2
1/10
Criterion: Is higher POPC density concentrated along the outer side of the curved membrane in both images?
Judge's Assessment: In the ground truth, higher POPC density is visibly concentrated along the outer side of the curved membrane (warmer colors preferentially on the outer arc of the wavy band). In the result, density is broadly and almost uniformly distributed over the whole rectangle, without an identifiable curved membrane or a distinguishable 'outer side' to compare; no clear outer-side enrichment pattern is present.

Overall Assessment

The result does not reproduce the curved membrane-band heatmap appearance seen in the ground truth, and consequently does not show the expected outer-side POPC density enrichment along the curved membrane. The result looks like an unmasked/global XY density histogram rather than a density mapped onto the curved membrane surface.

πŸ–ΌοΈ Visualization Comparison - Set 4

Ground Truth

Ground Truth 4

Agent Result

Result 4

Score Summary

Total Score
1/30
Goals
3
Points/Goal
10
Goal 1
1/10
Criterion: Do both plots show enrichment values plotted against membrane mean curvature?
Judge's Assessment: Ground truth includes a plot with relative enrichment (y-axis) versus mean curvature (x-axis). In the provided result images, one is a 2D density heatmap (POPC) with axes X/Y in nm and no curvature axis; it does not plot enrichment vs mean curvature. Because the expected enrichment-vs-curvature relationship is not shown in the result set (only a heatmap is shown), this criterion is not met.
Goal 2
0/10
Criterion: Are two curves corresponding to POPC and CDL0 visible in both plots?
Judge's Assessment: The ground truth enrichment plot shows two distinct curves/series: POPC (blue) and CDL0 (orange). The result image shown is a single POPC density heatmap and contains no POPC+CDL0 enrichment curves at all. Thus, two curves corresponding to POPC and CDL0 are not visible in the result.
Goal 3
0/10
Criterion: Is a horizontal reference line around enrichment = 1 present in both plots?
Judge's Assessment: The ground truth enrichment plot includes a horizontal dashed reference line at relative enrichment = 1. The result image shown (2D POPC density heatmap) has no enrichment axis and no horizontal reference line at 1. This requirement is not addressed in the result.

Overall Assessment

Compared to the ground truth, the provided result images do not include the key relative-enrichment-versus-mean-curvature plot. Instead, the visible result is a POPC 2D density heatmap, which cannot satisfy criteria about enrichment curves and the enrichment=1 reference line. As a result, only minimal credit is given, since the required enrichment-vs-curvature visualization elements are absent.

Score

40/50 (80.0%)

Questions & Correct Answers

1. Q1 correct answer: No (the trajectory contains 2000 frames). 2. Q2 correct answer: No (the lipid ratio is 9:1). 3. Q3 correct answer: Yes (CDL0 lipids enrich in negatively curved regions). 4. Q4 correct answer: Yes (relative density varies roughly between 0.8 and 1.3). 5. Q5 correct answer: No (POPC lipids enrich in positively curved regions, not negative).

Agent's Answers

Q1: Are there more than 3000 frames in the trajectory? no Q2: Is the ratio of POPC lipids to the neutral cardiolipin (CDL0) 8:1? no Q3: Do the CDL0 lipids enrich in the negatively curved membrane regions? yes Q4: Does the total lipid density change significantly with membrane mean curvature? no Q5: Do the POPC lipids enrich in the negatively curved membrane regions? no

Judge's Evaluation

Evaluation:

Q1 (10/10): Answered "no," which matches the criterion (trajectory has 2000 frames, so not more than 3000). Q2 (10/10): Answered "no," which matches the criterion (ratio is 9:1, not 8:1). Q3 (10/10): Answered "yes," which matches the criterion (CDL0 enriches in negatively curved membrane regions). Q4 (0/10): Answered "no," but the criterion says "yes"β€”total lipid relative density changes with mean curvature (varies roughly 0.8 to 1.3). This is a direct contradiction. Q5 (10/10): Answered "no," which matches the criterion (POPC enriches in positively curved regions, not negatively curved regions).

πŸ“Š Detailed Metrics

Visualization Quality
28/110
Output Generation
5/5
Efficiency
5/10
Text Q&A Score
40/50
80.0%