| Sequence | GCGGAGGGCCGGGTGGGC |
| Rev. Sequence | GCCCACCCGGCCCTCCGC |
| Type | DNA |
| SubType | B |
| Chains | duplex |
| Pdb | - |
| Ligands | No |
| Keywords | DNA-B Duplex Naked |
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 0.00000000 1719878400 |
| Simulated Time | 1,000 |
| Time Step | 20 ps |
| Parts | DNA |
| Temperature | 298K |
| Water | No |
| Additional Solvent | No |
| Counter Ions | No |
| Ionic Concentration | No |
| Additional Ions | No |
| Additional Molecules | No |
| Ions Parameters | No |
| Simulation Metadata (UMM) | |
|---|---|
| AdditionalIons | No |
| AdditionalMolecules | No |
| AdditionalSolvent | No |
| Author | D.F. |
| Chains | duplex |
| Comments | CGeNArate: A Sequence-Dependent Coarse-Grained Model of DNA for Accurate Atomistic MD Simulations of kb-long Duplexes, DOI: 10.1093/nar/gkae444 |
| CounterIons | No |
| Format | mdcrd |
| FrameStep | 20 ps |
| Frames | 50000 |
| IonicConcentration | No |
| IonsParameters | No |
| Ligands | No |
| NucType | DNA |
| PDB | NONE |
| Parts | DNA |
| RMSd_avg | 2.612 |
| RMSd_stdev | 0.538 |
| Rgyr_avg | 18.763 |
| Rgyr_stdev | 0.413 |
| SASA_avg | 3200.165 |
| SASA_stdev | 17.831 |
| SubType | B |
| Temperature | 298K |
| Topology | Simulated8.pdb |
| Trajectory | Simulated8aligned.mdcrd |
| Water | No |
| _id | NAFlex_miniABC_8_CG |
| dataset | Array |
| date | 0.00000000 1719878400 |
| description | DNA-B Duplex Naked |
| forceField | CGeNArate |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | GCCCACCCGGCCCTCCGC |
| saltConcentration | - |
| sequence | GCGGAGGGCCGGGTGGGC |
| soluteAtoms | 36 |
| soluteCharge | - |
| soluteResidues | 36 |
| solventAtoms | - |
| solventResidues | - |
| time | 1,000 |
| totalAtoms | 36 |
| totalCharge | - |
| totalIons | - |
| totalResidues | 36 |
| Quality Control | |
|---|---|
| RMSd | - |
| Rgyr | - |
| SASA | - |
| RMSf | - |