Update molecular cases with LFS tracking for large files

- Add .xtc, .gro, .jpg, .jpeg to LFS tracking
- Reorganize molecular visualization workflows

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

.gitattributes

@@ -13,4 +13,7 @@
 *.cif filter=lfs diff=lfs merge=lfs -text
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.nc filter=lfs diff=lfs merge=lfs -text
-bioimage_data/GS/dataset_002_zoom.jpg filter=lfs diff=lfs merge=lfs -text
+*.xtc filter=lfs diff=lfs merge=lfs -text
+*.gro filter=lfs diff=lfs merge=lfs -text
+*.jpg filter=lfs diff=lfs merge=lfs -text
+*.jpeg filter=lfs diff=lfs merge=lfs -text

eval_cases/molecular_vis/README.md

@@ -1,29 +0,0 @@
-# SciVisAgentBench: Molecular Visualization
-
-This benchmark is designed to evaluate agents on molecular visualization tasks, specifically focusing on tools like VMD (Visual Molecular Dynamics).
-
-## Overview
-
-The benchmark assesses agent capabilities across different levels of complexity:
-- **Basic Actions (Easy)**: Simple, atomic commands and operations (Currently implemented).
-- **Workflows (Medium)**: Sequences of actions forming a coherent pipeline (Planned).
-- **Scientific Tasks (Hard)**: Complex, goal-oriented scientific analysis and visualization (Planned).
-
-## Setup
-
-1. **Data Preparation**:
-   - Download the PDB file `1CRN` from the [RCSB PDB](https://www.rcsb.org/structure/1CRN).
-   - Place the downloaded file into the `data/` folder in this directory.
-
-## Usage
-
-You can run the evaluation cases defined in the YAML files (located in the `actions/` directory) using either:
-- **Promptfoo**
-- The **SciVisAgentBench Evaluation Framework**
-
-Refer to the [main repository](https://github.com/KuangshiAi/SciVisAgentBench/tree/main) for detailed instructions on running the evaluation harness.
-
-## Future Extensions
-
-### SciVisAgentBench: MD Simulations
-A placeholder for Molecular Dynamics (MD) simulation tasks is currently reserved. This will be expanded to include setting up, running, and analyzing simulations.

eval_cases/molecular_vis/eval_analysis_tasks.yaml

@@ -0,0 +1,158 @@
+# Test Cases for SciVisAgentBench molecular visualization workflows
+# This test evaluates the ability to complete molecular visualization tasks
+# with detailed requirements and evaluation criteria
+
+#simple licorice visualization of a protein 
+- vars:
+    question: |
+        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".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Q1 correct answer: Yes
+      rs-file: "md_analysis/results/answers_basic_vis.txt"
+
+#simple coloring by element of a protein
+- vars:
+    question: |
+        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".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Q1 correct answer: Yes
+      rs-file: "md_analysis/results/answers_element_coloring.txt"
+
+#simple selection and coloring of a protein
+- vars:
+    question: |
+        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".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Q1 correct answer: Yes
+      rs-file: "md_analysis/results/answers_selection_coloring.txt"
+
+#simple coloring by charge of a protein
+- vars:
+    question: |
+        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".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Q1 correct answer: Yes
+      rs-file: "md_analysis/results/answers_charge_coloring.txt"
+
+#simple selection and coloring of specific atoms
+- vars:
+    question: |
+        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".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Q1 correct answer: Yes
+      rs-file: "md_analysis/results/answers_complex_selection.txt"
+
+#simple selection and coloring of aromatic residues
+- vars:
+    question: |
+        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".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Q1 correct answer: Yes
+      rs-file: "md_analysis/results/answers_aromatic_selection.txt"
+
+#simple RMSD and RMSF calculation of a protein
+- vars:
+    question: |
+        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".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Does the output report the calculated RMSD?
+          2. Does the output report the calculated RMSF values or state that it requires a trajectory?
+      rs-file: "md_analysis/results/answers_rmsd_rmsf.txt"
+
+#simple radius of gyration calculation of a protein
+- vars:
+    question: |
+        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".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Does the output report a numeric value for the calculated Radius of Gyration?
+      rs-file: "md_analysis/results/answers_rg.txt"
+
+- vars:
+    question: |
+        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".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          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?
+      rs-file: "md_analysis/results/answers_distances_angles.txt"
+
+#simple contact calculation of a protein
+- vars:
+    question: |
+        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".
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Does the output report a numeric count of contacts?
+      rs-file: "md_analysis/results/answers_native_contacts.txt"

eval_cases/molecular_vis/eval_analysis_workflows.yaml

@@ -1,163 +1,48 @@
-# Test Cases for SciVisAgentBench molecular visualization workflows
-# This test evaluates the ability to complete molecular visualization tasks
-# with detailed requirements and evaluation criteria
-
-#simple licorice visualization of a protein 
-- vars:
-    question: |
-        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".
-  assert:
-    - type: llm-rubric
-      subtype: text
-      value: |
-          1. Q1 correct answer: Yes
-      rs-file: "md_analysis/results/answers_basic_vis.txt"
-
-#simple coloring by element of a protein
+# 1. RAS-RAF on a plasma membrane
+# The RAS protein is lipid anchored and sits on the inner leaflet of the plasma membrane where it can bind RAF.
+# This is a snapshot of a RAS protein bound to the RBD and CRD domains of RAF on top of an eight-component plasma membrane setup with the coarse-grained Martini 2 force field.
+# This simulation frame is an example from the following study https://doi.org/10.1073/pnas.2113297119 and can be found online at: https://bbs.llnl.gov/data/ras-lipid-dependent-dynamics-data
 - vars:
     question: |
-        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".
-  assert:
-    - type: llm-rubric
-      subtype: text
-      value: |
-          1. Q1 correct answer: Yes
-      rs-file: "md_analysis/results/answers_element_coloring.txt"
+        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.
 
-#simple selection and coloring of a protein
-- vars:
-    question: |
-        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".
-  assert:
-    - type: llm-rubric
-      subtype: text
-      value: |
-          1. Q1 correct answer: Yes
-      rs-file: "md_analysis/results/answers_selection_coloring.txt"
+        3. Analyze the visualization and answer the following questions:
+        Q1: Are there any cholesterol head groups in the bilayer center? (yes/no)
 
-#simple coloring by charge of a protein
-- vars:
-    question: |
-        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".
-  assert:
-    - type: llm-rubric
-      subtype: text
-      value: |
-          1. Q1 correct answer: Yes
-      rs-file: "md_analysis/results/answers_charge_coloring.txt"
+        Q2: How many lipids are there within 1.5 nm of the RAF protein?
+          A. 0
+          B. 0-3
+          C. 3-5
+          D. >5
 
-#simple selection and coloring of specific atoms
-- vars:
-    question: |
-        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".
+        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".
   assert:
     - type: llm-rubric
-      subtype: text
+      subtype: vision
       value: |
-          1. Q1 correct answer: Yes
-      rs-file: "md_analysis/results/answers_complex_selection.txt"
-
-#simple selection and coloring of aromatic residues
-- vars:
-    question: |
-        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".
-  assert:
+          1. Camera Position: Is the image centered on a protein complex composed of clearly distinguishable half red RAS and half blue RAF components?
+          2. Membrane Placement: Is a lipid bilayer clearly visible above the protein?
+          3. Correct Leaflet Ordering: Is the inner leaflet of the bilayer closer to the protein and the outer leaflet positioned farther away?
     - type: llm-rubric
       subtype: text
       value: |
           1. Q1 correct answer: Yes
-      rs-file: "md_analysis/results/answers_aromatic_selection.txt"
-
-#simple RMSD and RMSF calculation of a protein
-- vars:
-    question: |
-        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".
-  assert:
-    - type: llm-rubric
-      subtype: text
-      value: |
-          1. Does the output report the calculated RMSD?
-          2. Does the output report the calculated RMSF values or state that it requires a trajectory?
-      rs-file: "md_analysis/results/answers_rmsd_rmsf.txt"
-
-#simple radius of gyration calculation of a protein
-- vars:
-    question: |
-        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".
-  assert:
-    - type: llm-rubric
-      subtype: text
-      value: |
-          1. Does the output report a numeric value for the calculated Radius of Gyration?
-      rs-file: "md_analysis/results/answers_rg.txt"
-
-- vars:
-    question: |
-        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".
-  assert:
-    - type: llm-rubric
-      subtype: text
-      value: |
-          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?
-      rs-file: "md_analysis/results/answers_distances_angles.txt"
+          2. Q2 correct answer: C. 3-5
 
-#simple contact calculation of a protein
-- vars:
-    question: |
-        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".
-  assert:
-    - type: llm-rubric
-      subtype: text
-      value: |
-          1. Does the output report a numeric count of contacts?
-      rs-file: "md_analysis/results/answers_native_contacts.txt"
+# Q1 reason: quite some gray dots from cholesterol ROH headgroup bead can be seen in the center of the bilayer, so the answer is YES.
+# Q2 reason: if you run the flowing VMD selection command (name PO4 ROH) and within 15 of (index 3457 to 35009 and resid 188 to 329)
+# You will find 4 lipids head group beads, so the answer is C. 3-5 
+# Note here it’s important to only count each lipid once, e.g. either use a single reference bead per lipid or center of mass, also selecting the protein can be tricky as the lipids and water also if resid’s in the 188 to 329 range so either exclude other molecule or sub select only the protein residues
 
-# 1. Curved membrane simulation
+# 2. Curved membrane simulation
 # As part of a protocol paper for building membrane using the coarse-grained Martini 3 force field, https://doi.org/10.1016/bs.mie.2024.03.010, a tutorial was developed: https://bbs.llnl.gov/data/building-membranes-data
 # Tutorial 4 is on curved membranes which is used here as an example of bilayer visualization. 
 - vars:
@@ -186,47 +71,93 @@
 
 # Q1 reason: A few water molecules can be seen a little into the membrane.
 
-
-# 2. RAS-RAF on a plasma membrane
-# The RAS protein is lipid anchored and sits on the inner leaflet of the plasma membrane where it can bind RAF.
-# This is a snapshot of a RAS protein bound to the RBD and CRD domains of RAF on top of an eight-component plasma membrane setup with the coarse-grained Martini 2 force field.
-# This simulation frame is an example from the following study https://doi.org/10.1073/pnas.2113297119 and can be found online at: https://bbs.llnl.gov/data/ras-lipid-dependent-dynamics-data
+# 3. Curved membrane trajectory inspection
 - vars:
     question: |
-        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.
+        1. Please load the Martini coarse-grained membrane simulation from
+        "trajectory-inspection/data/trajectory-inspection.gro" into VMD.
 
-        3. Analyze the visualization and answer the following questions:
-        Q1: Are there any cholesterol head groups in the bilayer center? (yes/no)
+        2. Load the trajectory file
+        "trajectory-inspection/data/trajectory-inspection_3to5us.xtc".
 
-        Q2: How many lipids are there within 1.5 nm of the RAF protein?
-          A. 0
-          B. 0-3
-          C. 3-5
-          D. >5
+        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 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".
 
-        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".
   assert:
     - type: llm-rubric
       subtype: vision
+      gs_file: trajectory-inspection/GS/membrane-curved-tilted-side-5us.jpg
+      rs_file: trajectory-inspection/results/{agent_mode}/membrane-curved-tilted-side-5us.jpg
       value: |
-          1. Camera Position: Is the image centered on a protein complex composed of clearly distinguishable half red RAS and half blue RAF components?
-          2. Membrane Placement: Is a lipid bilayer clearly visible above the protein?
-          3. Correct Leaflet Ordering: Is the inner leaflet of the bilayer closer to the protein and the outer leaflet positioned farther away?
+          1. Do both images show a side view of a curved lipid bilayer rather than a top-down view?
+          2. Are two lipid species visible with different colors, corresponding to POPC and CDL0 PO4 beads?
+          3. Does the membrane visibly undulate, with one lipid type enriched on the inner curvature and the other on the outer curvature?
+
     - type: llm-rubric
-      subtype: text
+      subtype: vision
+      gs_file: trajectory-inspection/GS/avg_2d_dens_CDL0.png
+      rs_file: trajectory-inspection/results/{agent_mode}/avg_2d_dens_CDL0.png
       value: |
-          1. Q1 correct answer: Yes
-          2. Q2 correct answer: C. 3-5
+          1. Do both images show a curved membrane band visualized as a heatmap density map?
+          2. Are sampling markers or dots visible along the membrane surface in both images?
+          3. Is higher CDL0 density concentrated along the inner side of the curved membrane in both images?
 
-# Q1 reason: quite some gray dots from cholesterol ROH headgroup bead can be seen in the center of the bilayer, so the answer is YES.
-# Q2 reason: if you run the flowing VMD selection command (name PO4 ROH) and within 15 of (index 3457 to 35009 and resid 188 to 329)
-# You will find 4 lipids head group beads, so the answer is C. 3-5 
-# Note here it’s important to only count each lipid once, e.g. either use a single reference bead per lipid or center of mass, also selecting the protein can be tricky as the lipids and water also if resid’s in the 188 to 329 range so either exclude other molecule or sub select only the protein residues
+    - type: llm-rubric
+      subtype: vision
+      gs_file: trajectory-inspection/GS/avg_2d_dens_POPC.png
+      rs_file: trajectory-inspection/results/{agent_mode}/avg_2d_dens_POPC.png
+      value: |
+          1. Do both images show a curved membrane band represented as a heatmap density map?
+          2. Are sampling markers or dots visible along the membrane surface in both images?
+          3. Is higher POPC density concentrated along the outer side of the curved membrane in both images?
+
+    - type: llm-rubric
+      subtype: vision
+      gs_file: trajectory-inspection/GS/relative_enrichment.png
+      rs_file: trajectory-inspection/results/{agent_mode}/relative_enrichment.png
+      value: |
+          1. Do both plots show enrichment values plotted against membrane mean curvature?
+          2. Are two curves corresponding to POPC and CDL0 visible in both plots?
+          3. Is a horizontal reference line around enrichment = 1 present in both plots?
+
+    - type: llm-rubric
+      subtype: text
+      value: |
+          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).

molecular_vis/curved-membrane/data/curved-membrane.gro

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+version https://git-lfs.github.com/spec/v1
+oid sha256:13037008ccc807f7ad86da3e222a0d632841a3fbb1cd04b55cd0dcf3336ed67a
+size 1106890

molecular_vis/ras-raf-membrane/data/ras-raf-membrane.gro

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+version https://git-lfs.github.com/spec/v1
+oid sha256:0e7083794405852ca2a273ba9cd873cacb4f0327edbb373bb6bf222ff8f65ff3
+size 9401161

molecular_vis/trajectory-inspection/data/trajectory-inspection.gro

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+version https://git-lfs.github.com/spec/v1
+oid sha256:13037008ccc807f7ad86da3e222a0d632841a3fbb1cd04b55cd0dcf3336ed67a
+size 1106890

molecular_vis/trajectory-inspection/data/trajectory-inspection_3to5us.xtc

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+version https://git-lfs.github.com/spec/v1
+oid sha256:219812a2447c7e03851cdcb83af4486a6a1dae069cd40d7912609f903fed277a
+size 158624812

molecular_vis/trajectory-inspection/task_description.txt

@@ -0,0 +1,41 @@
+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 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".

molecular_vis/trajectory-inspection/visualization_goals.txt

@@ -0,0 +1,3 @@
+1. Do both images show a side view of a curved lipid bilayer rather than a top-down view?
+2. Are two lipid species visible with different colors, corresponding to POPC and CDL0 PO4 beads?
+3. Does the membrane visibly undulate, with one lipid type enriched on the inner curvature and the other on the outer curvature?