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将生物大模型、对接计算引擎与组学管线并排横向对比。按获取方式、硬件开销及细分领域灵活筛选，在一分钟内得出客观可辩护的技术选型方案。
| 技术参数指标 | ＋ 添加工具 | |||
|---|---|---|---|---|
| Category | Research Tooling & Frameworks | Scientific ML Libraries & Supporting Tools | Scientific ML Libraries & Supporting Tools | — |
| Subcategory | Molecular Dynamics Engines | Conventional or Statistical Baselines | Conventional or Statistical Baselines | — |
| Company | GROMACS Development Team | Research / method authors | Research / method authors | — |
| Access mode | Open Source | Confirm distribution and exact release | Confirm distribution and exact release | — |
| Licence conditions | LGPL-2.1 | NOT_INDEPENDENTLY_AUDITED | NOT_INDEPENDENTLY_AUDITED | — |
| Compute requirements | Multi-core CPU and NVIDIA/AMD GPU for accelerated PME electrostatics | Version and data dependent | Version and data dependent | — |
| Biological application | Biomolecular dynamics, membrane transport, protein folding, and drug-target residence time | 未明确记录 | 未明确记录 | — |
| Research workflow | PDB topology generation -> energy minimization -> equilibration -> production MD trajectory | 未明确记录 | 未明确记录 | — |
| Evidence level | Cited in over 30,000 peer-reviewed biophysics publications | PEER_REVIEWED_METHOD_OR_CONFERENCE | PEER_REVIEWED_METHOD_OR_CONFERENCE | — |
| Commercial eligibility | Permissive open source release | NOT_INDEPENDENTLY_AUDITED | NOT_INDEPENDENTLY_AUDITED | — |
| Price | Free Open Source | Verify access and licence | Verify access and licence | — |
| Availability ⓘ | Available via Bioconda and source compilation | Method paper or official documentation | Method paper or official documentation | — |
| Features | Unrivaled simulation throughput on modern x86/ARM CPUs and NVIDIA/AMD GPUs, Comprehensive support for standard force fields (AMBER, CHARMM, OPLS, GROMOS), Free energy calculation tools for relative binding affinity and alchemical transformations, Extensive trajectory analysis utilities for root-mean-square deviation, gyration, and hydrogen bonds | HMMER 3 scientific method, Query sequences or profile HMM and sequence database, Profile HMM hits and statistical homology significance | MMseqs2 scientific method, Amino acid queries and reference sequence database, Sequence matches, clusters and alignment results | — |
| Entry type | Open Source Software | Classical/statistical scientific method | Classical/statistical scientific method | — |
| AI role | Physical Molecular Dynamics Simulation | NON_AI_CLASSICAL | NON_AI_CLASSICAL | — |
| Input data | 未明确记录 | Query sequences or profile HMM and sequence database | Amino acid queries and reference sequence database | — |
| Output data | 未明确记录 | Profile HMM hits and statistical homology significance | Sequence matches, clusters and alignment results | — |
| Validation | 未明确记录 | Published method scope; no independent BioAtlas execution or benchmark | Published method scope; no independent BioAtlas execution or benchmark | — |
| Type | Molecular dynamics simulation engine | 未明确记录 | 未明确记录 | — |
| Intended use | 未明确记录 | 未明确记录 | 未明确记录 | — |
| Compatibility | 未明确记录 | 未明确记录 | 未明确记录 | — |
| Manufacturer | GROMACS Team & KTH Royal Institute of Technology | 未明确记录 | 未明确记录 | — |
| Integration evidence | https://www.gromacs.org | 未明确记录 | 未明确记录 | — |
| Laboratory handoff | Validates dynamic conformational stability of designed protein candidates | 未明确记录 | 未明确记录 | — |