{"record_type":"pith_number_record","schema_url":"https://pith.science/schemas/pith-number/v1.json","pith_number":"pith:2013:JIYIOZRGISVSTWOKODNDX65F7O","short_pith_number":"pith:JIYIOZRG","schema_version":"1.0","canonical_sha256":"4a3087662644ab29d9ca70da3bfba5fb9303760c916fd9edc1877a325d95b021","source":{"kind":"arxiv","id":"1307.5144","version":1},"attestation_state":"computed","paper":{"title":"Hamiltonian replica-exchange in GROMACS: a flexible implementation","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cond-mat.stat-mech","physics.bio-ph","physics.chem-ph"],"primary_cat":"physics.comp-ph","authors_text":"Giovanni Bussi","submitted_at":"2013-07-19T07:36:06Z","abstract_excerpt":"A simple and general implementation of Hamiltonian replica exchange for the popular molecular-dynamics software GROMACS is presented. In this implementation, arbitrarily different Hamiltonians can be used for the different replicas without incurring in any significant performance penalty. The implementation was validated on a simple toy model - alanine dipeptide in water - and applied to study the rearrangement of an RNA tetraloop, where it was used to compare recently proposed force-field corrections."},"verification_status":{"content_addressed":true,"pith_receipt":true,"author_attested":false,"weak_author_claims":0,"strong_author_claims":0,"externally_anchored":false,"storage_verified":false,"citation_signatures":0,"replication_records":0,"graph_snapshot":true,"references_resolved":false,"formal_links_present":false},"canonical_record":{"source":{"id":"1307.5144","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.comp-ph","submitted_at":"2013-07-19T07:36:06Z","cross_cats_sorted":["cond-mat.stat-mech","physics.bio-ph","physics.chem-ph"],"title_canon_sha256":"bc10b0021ee01d5dc0709306dc8981b16b89e0e1d60671ca09793d057b48ec1a","abstract_canon_sha256":"b26d83ad3e8751bd7c60fa3f1215938cb68e3448b8404d4eb070065233e0428d"},"schema_version":"1.0"},"receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T02:41:42.289469Z","signature_b64":"TEqcKvjYagML1mKLJWyOMAdtEkjOpZ4nG9dMTemeulbOF680rmKLBc/ZMOHnExCm9aBtmnlO9MIgubof3U7iAA==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"4a3087662644ab29d9ca70da3bfba5fb9303760c916fd9edc1877a325d95b021","last_reissued_at":"2026-05-18T02:41:42.288931Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T02:41:42.288931Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"graph_snapshot":{"paper":{"title":"Hamiltonian replica-exchange in GROMACS: a flexible implementation","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cond-mat.stat-mech","physics.bio-ph","physics.chem-ph"],"primary_cat":"physics.comp-ph","authors_text":"Giovanni Bussi","submitted_at":"2013-07-19T07:36:06Z","abstract_excerpt":"A simple and general implementation of Hamiltonian replica exchange for the popular molecular-dynamics software GROMACS is presented. In this implementation, arbitrarily different Hamiltonians can be used for the different replicas without incurring in any significant performance penalty. The implementation was validated on a simple toy model - alanine dipeptide in water - and applied to study the rearrangement of an RNA tetraloop, where it was used to compare recently proposed force-field corrections."},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1307.5144","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"},"aliases":[{"alias_kind":"arxiv","alias_value":"1307.5144","created_at":"2026-05-18T02:41:42.289003+00:00"},{"alias_kind":"arxiv_version","alias_value":"1307.5144v1","created_at":"2026-05-18T02:41:42.289003+00:00"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1307.5144","created_at":"2026-05-18T02:41:42.289003+00:00"},{"alias_kind":"pith_short_12","alias_value":"JIYIOZRGISVS","created_at":"2026-05-18T12:27:49.015174+00:00"},{"alias_kind":"pith_short_16","alias_value":"JIYIOZRGISVSTWOK","created_at":"2026-05-18T12:27:49.015174+00:00"},{"alias_kind":"pith_short_8","alias_value":"JIYIOZRG","created_at":"2026-05-18T12:27:49.015174+00:00"}],"events":[],"event_summary":{},"paper_claims":[],"inbound_citations":{"count":0,"internal_anchor_count":0,"sample":[]},"formal_canon":{"evidence_count":0,"sample":[],"anchors":[]},"links":{"html":"https://pith.science/pith/JIYIOZRGISVSTWOKODNDX65F7O","json":"https://pith.science/pith/JIYIOZRGISVSTWOKODNDX65F7O.json","graph_json":"https://pith.science/api/pith-number/JIYIOZRGISVSTWOKODNDX65F7O/graph.json","events_json":"https://pith.science/api/pith-number/JIYIOZRGISVSTWOKODNDX65F7O/events.json","paper":"https://pith.science/paper/JIYIOZRG"},"agent_actions":{"view_html":"https://pith.science/pith/JIYIOZRGISVSTWOKODNDX65F7O","download_json":"https://pith.science/pith/JIYIOZRGISVSTWOKODNDX65F7O.json","view_paper":"https://pith.science/paper/JIYIOZRG","resolve_alias":"https://pith.science/api/pith-number/resolve?arxiv=1307.5144&json=true","fetch_graph":"https://pith.science/api/pith-number/JIYIOZRGISVSTWOKODNDX65F7O/graph.json","fetch_events":"https://pith.science/api/pith-number/JIYIOZRGISVSTWOKODNDX65F7O/events.json","actions":{"anchor_timestamp":"https://pith.science/pith/JIYIOZRGISVSTWOKODNDX65F7O/action/timestamp_anchor","attest_storage":"https://pith.science/pith/JIYIOZRGISVSTWOKODNDX65F7O/action/storage_attestation","attest_author":"https://pith.science/pith/JIYIOZRGISVSTWOKODNDX65F7O/action/author_attestation","sign_citation":"https://pith.science/pith/JIYIOZRGISVSTWOKODNDX65F7O/action/citation_signature","submit_replication":"https://pith.science/pith/JIYIOZRGISVSTWOKODNDX65F7O/action/replication_record"}},"created_at":"2026-05-18T02:41:42.289003+00:00","updated_at":"2026-05-18T02:41:42.289003+00:00"}