Entry: NAFlex_implSolvMD_CG
Nucleic Acid Data:
| Sequence | GCAACGTGCTATGGAAGC |
| Rev. Sequence | GCTTCCATAGCACGTTGC |
| Type | DNA |
| SubType | B |
| Chains | duplex |
| Pdb | - |
| Ligands | No |
| Keywords | DNA-B Duplex Naked |
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | CGeNArate |
| Simulation Date | 2024-Jul-09 |
| Simulated Time | 1,000 ns |
| 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 |
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
(Click to see full UMM)
| 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 | netcdf |
| FrameStep | 20 ps |
| Frames | 50000 |
| IonicConcentration | No |
| IonsParameters | No |
| Ligands | No |
| NucType | DNA |
| PDB | NONE |
| Parts | DNA |
| RMSd_avg | 3.697 |
| RMSd_stdev | 0.900 |
| Rgyr_avg | 18.519 |
| Rgyr_stdev | 0.885 |
| SASA_avg | 6203.937 |
| SASA_stdev | 186.446 |
| SubType | B |
| Temperature | 298K |
| Topology | AtomACGT.pdb |
| Trajectory | AtomACGTAll_reduced.nc |
| Water | No |
| _id | NAFlex_implSolvMD_CG |
| dataset | Array |
| date | 2024-Jul-09 |
| description | DNA-B Duplex Naked |
| forceField | CGeNArate |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | GCTTCCATAGCACGTTGC |
| saltConcentration | - |
| sequence | GCAACGTGCTATGGAAGC |
| soluteAtoms | 1140 |
| soluteCharge | -34 |
| soluteResidues | 36 |
| solventAtoms | - |
| solventResidues | - |
| time | 1,000 |
| totalAtoms | 1140 |
| totalCharge | -34 |
| totalIons | - |
| totalResidues | 36 |
| Quality Control | |
|---|---|
| RMSd | 3.697 (0.900) Å  |
| Rgyr | 18.519 (0.885) Å  |
| SASA | 6203.937 (186.446) Ų  |
| RMSf |  |