Paper Citation Record · LEDGER

Automating MD simulations for Proteins using Large language Models: NAMD-Agent

As of 8 August 2026, this Paper Citation Record lists 53 of 53 outbound references and 5 inbound Pith citation observations for arXiv:2507.07887.

A citation records a reference. It does not transfer a finding from one paper to another.

pith.paper-citation-record.v1
2507.07887 v1

Coverage vector

measured 53 of 53 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-06T18:33:54.100493Z

measured 58 of 58 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-08T06:32:00.761636+00:00

measured 5 of 5 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links, observed 2026-06-27T07:08:05.736109Z

measured 1 of 1 external citation measurements

A source-named dated measurement, never combined with another source.

Source: arxiv_reference, observed 2026-08-05T02:28:24.338817Z

Reference resolution

53 of 53 outbound references displayed

verified exact5
verified fuzzy16
unresolved29
parse uncertain0
malformed identifier3
metadata mismatch0

External citation measurements

1
arxiv_reference, observed 2026-08-05T02:28:24.338817Z

Outbound references

Observation 64839b72-d472-4d3b-8cca-11eefb967555 · outbound

This paper cites Vaswani, N.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Vaswani, N

Reference 1

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T18:34:01.147661Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 824b3b5c-567c-43f7-97d5-51c2d1de3853 · outbound

This paper cites McTear, Conversational ai: Dialogue systems, conversational agents, and chatbots, Springer Nature, 2022.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent McTear, Conversational ai: Dialogue systems, conversational agents, and chatbots, Springer Nature, 2022

Reference 2

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T18:34:00.905150Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation c2977497-8304-432f-a2d7-7d607e3cf97a · outbound

This paper cites an unresolved cited work.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Unresolved cited work

Reference 3

Resolution: unresolved; raw_fallback, observed 2026-08-06T18:34:00.643713Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 0cd931d8-5ce8-4f0e-9bf0-1973370985c3 · outbound

This paper cites Van Veen, C.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Van Veen, C

Reference 4

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T18:34:00.445999Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 6e6d7afe-101e-4cf2-849a-0989a9e9a0a2 · outbound

This paper cites Team, et al., Scaling neural machine translation to 200 languages, Nature 630 (8018) (2024) 841.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Team, et al., Scaling neural machine translation to 200 languages, Nature 630 (8018) (2024) 841

Reference 5

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T18:34:00.242267Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 7813c235-3997-4d60-a195-ea823ca01def · outbound

This paper cites Agent AI: Surveying the Horizons of Multimodal Interaction.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Agent AI: Surveying the Horizons of Multimodal Interaction

Reference 6

Resolution: unresolved; no resolver link, observed 2026-08-06T18:33:50.775261Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation dbe679e9-0105-4496-ba21-abe0827311c0 · outbound

This paper cites an unresolved cited work.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Unresolved cited work

Reference 7

Resolution: unresolved; raw_fallback, observed 2026-08-06T18:33:59.970203Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation b3a2780b-c813-4ab7-8083-66321ecbdbb6 · outbound

This paper cites an unresolved cited work.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Unresolved cited work

Reference 8

Resolution: unresolved; raw_fallback, observed 2026-08-06T18:33:59.786365Z

Source-reported events for the cited work

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Observation 6a0bf463-8217-4bd2-9801-9aa7039cec18 · outbound

This paper cites URLhttps://github.com/SeleniumHQ/selenium.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent URLhttps://github.com/SeleniumHQ/selenium

Reference 9

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T18:33:59.480347Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 7f4694de-8f6b-4d60-ac9b-77117596900d · outbound

This paper cites Jadhav, P.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Jadhav, P

Reference 10

Resolution: unresolved; no resolver link, observed 2026-08-06T18:33:51.064831Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 5726b7f4-a58d-4ff0-a3b6-3dd8978967d6 · outbound

This paper cites Adsorb-Agent: Autonomous Identification of Stable Adsorption Configurations via Large Language Model Agent.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Adsorb-Agent: Autonomous Identification of Stable Adsorption Configurations via Large Language Model Agent

Reference 11

Resolution: unresolved; no resolver link, observed 2026-08-06T18:33:51.119780Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation a3d2b163-99c1-4ebd-bf2f-1df535a4ff03 · outbound

This paper cites LLM-Drone: Aerial Additive Manufacturing with Drones Planned Using Large Language Models.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent LLM-Drone: Aerial Additive Manufacturing with Drones Planned Using Large Language Models

Reference 12

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Source-reported events for the cited work

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Observation 001e7677-d87d-4691-b7f6-bffcb84e313d · outbound

This paper cites Chaudhari, J.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Chaudhari, J

Reference 13

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T18:33:59.334251Z

Source-reported events for the cited work

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Observation ec3fcc54-be4e-46da-ac7b-f7f98b51d2d0 · outbound

This paper cites an unresolved cited work.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Unresolved cited work

Reference 14

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Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 56bc4285-be29-46fe-94d2-7b879b9b94fc · outbound

This paper cites an unresolved cited work.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Unresolved cited work

Reference 15

Resolution: unresolved; raw_fallback, observed 2026-08-06T18:33:59.207898Z

Source-reported events for the cited work

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Observation f8219e2b-c57d-4443-870b-20a245458154 · outbound

This paper cites Singh, A.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Singh, A

Reference 16

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Source-reported events for the cited work

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Observation afe6cda5-0c2e-4cef-87e3-34d7249978c6 · outbound

This paper cites Suplatov, Y.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Suplatov, Y

Reference 17

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T18:33:58.969936Z

Source-reported events for the cited work

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Observation 13395433-fbf2-4975-9d61-575d43438a1e · outbound

This paper cites an unresolved cited work.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Unresolved cited work

Reference 18

Resolution: unresolved; raw_fallback, observed 2026-08-06T18:33:58.837371Z

Source-reported events for the cited work

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Observation 9411c23d-5754-4aea-ba82-0a1c1782a2a7 · outbound

This paper cites Carvalho Martins, E.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Carvalho Martins, E

Reference 19

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T18:33:58.699814Z

Source-reported events for the cited work

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Observation 7138bfa3-ce80-47f3-a56d-88c08992472c · outbound

This paper cites MDCrow: Automating Molecular Dynamics Workflows with Large Language Models.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent MDCrow: Automating Molecular Dynamics Workflows with Large Language Models

Reference 20

Resolution: unresolved; no resolver link, observed 2026-08-06T18:33:51.712180Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 33d79090-d7cd-4be4-921b-4c0bcd551424 · outbound

This paper cites an unresolved cited work.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Unresolved cited work

Reference 21

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Source-reported events for the cited work

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Observation 8ecb03ac-a8ef-40f2-86e4-44e511ef0556 · outbound

This paper cites Agentic AI for Scientific Discovery: A Survey of Progress, Challenges, and Future Directions.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Agentic AI for Scientific Discovery: A Survey of Progress, Challenges, and Future Directions

Reference 22

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Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation f4a8c0b7-9c37-4877-9be3-47b2e92f286a · outbound

This paper cites Liu, Llamaindex.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Liu, Llamaindex

Reference 23

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T18:33:58.460764Z

Source-reported events for the cited work

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Observation a3db284e-66c9-4bec-bace-cc25ad808283 · outbound

This paper cites ReAct: Synergizing Reasoning and Acting in Language Models.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent ReAct: Synergizing Reasoning and Acting in Language Models

Reference 24

Resolution: unresolved; no resolver link, observed 2026-08-06T18:33:52.019252Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 6857cf4d-d2d5-4226-9bd9-04faccaca1e5 · outbound

This paper cites AutoGen: Enabling Next-Gen LLM Applications via Multi-Agent Conversation.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent AutoGen: Enabling Next-Gen LLM Applications via Multi-Agent Conversation

Reference 25

Resolution: unresolved; no resolver link, observed 2026-08-06T18:33:52.065688Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 7cf2fbce-adf8-4c31-9b87-a7097b2d8dd2 · outbound

This paper cites Eastman, O.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Eastman, O

Reference 26

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T18:33:58.327607Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation fbb132b2-72c5-4238-b442-7959a3331039 · outbound

This paper cites an unresolved cited work.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Unresolved cited work

Reference 27

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Source-reported events for the cited work

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Observation fabbd107-4b5f-461b-8dd8-eb86c2378747 · outbound

This paper cites Kern, auto_cgui: Automatic charmm-gui browser interaction with python,https: //github.com/nk53/auto_cgui, version accessed on 2025-06-09, MIT license (2025).

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Kern, auto_cgui: Automatic charmm-gui browser interaction with python,https: //github.com/nk53/auto_cgui, version accessed on 2025-06-09, MIT license (2025)

Reference 28

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Source-reported events for the cited work

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Observation 6b15867d-0c55-459d-aa7d-9d9cd0d46051 · outbound

This paper cites an unresolved cited work.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Unresolved cited work

Reference 29

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Source-reported events for the cited work

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Observation 98a3ab02-dbb8-4663-9281-605c6c936b41 · outbound

This paper cites an unresolved cited work.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Unresolved cited work

Reference 30

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Observation 5ef4b05d-6afc-4ba5-91d7-7f190b12fff7 · outbound

This paper cites an unresolved cited work.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Unresolved cited work

Reference 31

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Observation d319a88a-42b9-4eeb-bd1e-a8fea7aa7eb7 · outbound

This paper cites Humphrey, A.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Humphrey, A

Reference 32

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Observation 1521c324-0198-43f8-b698-2dd7e9534e10 · outbound

This paper cites an unresolved cited work.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Unresolved cited work

Reference 33

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Source-reported events for the cited work

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Observation 2b833d8c-a2c7-431c-8213-a293aef59ac3 · outbound

This paper cites Eastman, J.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Eastman, J

Reference 34

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Source-reported events for the cited work

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Observation 7b9206dc-c7f2-4e1e-9b80-0fe79ec79d5c · outbound

This paper cites Lewis, E.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Lewis, E

Reference 35

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Source-reported events for the cited work

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Observation 2c37d754-62b6-454a-9720-5db83994c445 · outbound

This paper cites Toolformer: Language Models Can Teach Themselves to Use Tools.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Toolformer: Language Models Can Teach Themselves to Use Tools

Reference 36

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Observation 40a4a915-bca5-4181-9186-1f8e1433f206 · outbound

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Automating MD simulations for Proteins using Large language Models: NAMD-Agent Unresolved cited work

Reference 37

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Observation a8dac7d4-a816-40ef-b5fd-a45d224bad39 · outbound

This paper cites Augmented Language Models: a Survey.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Augmented Language Models: a Survey

Reference 38

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Source-reported events for the cited work

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Observation 446ffa45-2b08-43bd-b194-1f1406bbba67 · outbound

This paper cites Chandrasekhar, J.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Chandrasekhar, J

Reference 39

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Source-reported events for the cited work

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Observation 892495e6-e153-497a-81cd-5b3c36a56cee · outbound

This paper cites NANOGPT: A Query-Driven Large Language Model Retrieval-Augmented Generation System for Nanotechnology Research.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent NANOGPT: A Query-Driven Large Language Model Retrieval-Augmented Generation System for Nanotechnology Research

Reference 40

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Source-reported events for the cited work

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Observation 0fdc0192-0623-466b-9a52-f7d0dc1f3930 · outbound

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Automating MD simulations for Proteins using Large language Models: NAMD-Agent Unresolved cited work

Reference 41

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Observation eb62bd36-9b59-46d9-8e20-f648b692dc76 · outbound

This paper cites an unresolved cited work.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Unresolved cited work

Reference 42

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Observation af302790-1d3b-4304-9996-547e877119bd · outbound

This paper cites Code Llama: Open Foundation Models for Code.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Code Llama: Open Foundation Models for Code

Reference 43

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Source-reported events for the cited work

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Observation 9a33a0d5-af69-4f6c-9830-26f094dd381a · outbound

This paper cites Kabsch, A solution for the best rotation to relate two sets of vectors, Acta Crystal- lographica Section A 32 (1976) 922–923.doi:10.1107/S0567739476001873.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Kabsch, A solution for the best rotation to relate two sets of vectors, Acta Crystal- lographica Section A 32 (1976) 922–923.doi:10.1107/S0567739476001873

Reference 44

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Source-reported events for the cited work

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Observation b9bc9138-10e8-411e-9035-9b67da0cb1bb · outbound

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Automating MD simulations for Proteins using Large language Models: NAMD-Agent Karplus, J

Reference 45

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Source-reported events for the cited work

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Observation 81bc3ae8-3534-41fa-abb6-f23c3b3eb25a · outbound

This paper cites Amadei, A.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Amadei, A

Reference 46

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Observation e3178223-d252-4789-ad2f-bf4ae5a9a174 · outbound

This paper cites Seeliger, B.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Seeliger, B

Reference 47

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Observation 539fab9b-36ce-4387-bddd-e50e1177f289 · outbound

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Automating MD simulations for Proteins using Large language Models: NAMD-Agent Unresolved cited work

Reference 48

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Observation fca96224-5bbb-4c17-9350-0e22023d797c · outbound

This paper cites Shrake, J.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Shrake, J

Reference 49

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Source-reported events for the cited work

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Observation 5633b0e9-3651-44ea-9d1b-52ea3b1b83fa · outbound

This paper cites an unresolved cited work.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Unresolved cited work

Reference 50

Resolution: unresolved; raw_fallback, observed 2026-08-06T18:33:55.498187Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 75b09267-db37-4e4d-939d-efa97a6933ee · outbound

This paper cites an unresolved cited work.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Unresolved cited work

Reference 51

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Source-reported events for the cited work

correction dated 2005-09-22. Source: crossref record 10.1073/pnas.0507472102->10.1073/pnas.0403643101:correction, observed 2026-07-11T02:58:37.719817+00:00. This notice travels one citation hop only.

Observation 45932aa8-70a6-4e15-b91b-604fe05b0a88 · outbound

This paper cites an unresolved cited work.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Unresolved cited work

Reference 52

Resolution: verified exact; doi, observed 2026-08-06T18:33:54.220613Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 9b4c03a6-9a21-4529-b385-b14ef45f4777 · outbound

This paper cites an unresolved cited work.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent Unresolved cited work

Reference 53

Resolution: verified exact; raw_fallback, observed 2026-08-06T18:33:54.882694Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Pith citing papers

Observation 9f617e62-802b-4099-8307-cb50606f4f5b · inbound

El Agente Quntur: A research collaborator agent for quantum chemistry cites this paper.

El Agente Quntur: A research collaborator agent for quantum chemistry Automating MD simulations for Proteins using Large language Models: NAMD-Agent

Reference 64

Resolution: verified exact; arxiv_id, observed 2026-05-16T06:50:42.414133Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation dc1fbad7-8502-419b-a0f6-036b293fe030 · inbound

PolyJarvis: An LLM-Orchestrated Agent for Automated All-Atom Molecular Dynamics of Amorphous Homopolymers cites this paper.

PolyJarvis: An LLM-Orchestrated Agent for Automated All-Atom Molecular Dynamics of Amorphous Homopolymers Automating MD simulations for Proteins using Large language Models: NAMD-Agent

Reference 9

Resolution: verified exact; arxiv_id, observed 2026-05-13T21:18:17.278288Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 3585515e-5558-49e2-9e32-d64c81fe947f · inbound

In-situ process monitoring for defect detection in wire-arc additive manufacturing: an agentic AI approach cites this paper.

In-situ process monitoring for defect detection in wire-arc additive manufacturing: an agentic AI approach Automating MD simulations for Proteins using Large language Models: NAMD-Agent

Reference 108

Resolution: verified exact; arxiv_id, observed 2026-05-10T21:20:50.381469Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 43fabfc6-f001-4a46-aa79-669b6094139b · inbound

From Knowledge to Action: Outcomes of the 2025 Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry cites this paper.

From Knowledge to Action: Outcomes of the 2025 Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry Automating MD simulations for Proteins using Large language Models: NAMD-Agent

Reference 241

Resolution: metadata mismatch; arxiv_id, observed 2026-05-11T17:21:10.346284Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation ea845a2d-59c6-448a-afb2-cdbad3487c9e · inbound

MDForge: Agentic Molecular Dynamics Pipeline Design under Sparse Simulator Feedback cites this paper.

MDForge: Agentic Molecular Dynamics Pipeline Design under Sparse Simulator Feedback Automating MD simulations for Proteins using Large language Models: NAMD-Agent

Reference 3

Resolution: metadata mismatch; arxiv_id, observed 2026-07-03T14:18:22.738771Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.