Entry: NAFlex_Naked_DNA_RNA
Nucleic Acid Data:
| Sequence | CGCGAA |
| Rev. Sequence | TTCGCG |
| Type | DNA+RNA |
| SubType | B |
| Chains | duplex |
| Pdb | - |
| Ligands | No |
| Keywords | -B Duplex Naked SPC/E AddedSalt |
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 2022-Apr-28 |
| Simulated Time | 250 ns |
| Time Step | 20 ps |
| Parts | DNA+RNA+ions |
| Temperature | 298K |
| Water | SPCE |
| Additional Solvent | No |
| Counter Ions | Na+Cl- |
| Ionic Concentration | 0.05M |
| Additional Ions | No |
| Additional Molecules | No |
| Ions Parameters | Dang |
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 | V.G. |
| Chains | duplex |
| Comments | - |
| CounterIons | Na+Cl- |
| Format | xtc |
| FrameStep | 20 ps |
| Frames | 12500 |
| IonicConcentration | 0.05M |
| IonsParameters | Dang |
| Ligands | No |
| NucType | DNA+RNA |
| PDB | NONE |
| Parts | DNA+RNA+ions |
| RMSd_avg | 3.083 |
| RMSd_stdev | 0.717 |
| Rgyr_avg | 13.457 |
| Rgyr_stdev | 0.486 |
| SASA_avg | 4506.046 |
| SASA_stdev | 95.506 |
| SubType | B |
| Temperature | 298K |
| Topology | structure.stripped.top |
| Trajectory | structure.stripped.xtc |
| Water | SPCE |
| _id | NAFlex_Naked_DNA_RNA |
| dataset | Array |
| date | 2022-Apr-28 |
| description | -B Duplex Naked SPC/E AddedSalt |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Rna |
| rev_sequence | TTCGCG |
| saltConcentration | - |
| sequence | CGCGAA |
| soluteAtoms | 764 |
| soluteCharge | - |
| soluteResidues | 24 |
| solventAtoms | - |
| solventResidues | - |
| time | 250 |
| totalAtoms | 764 |
| totalCharge | - |
| totalIons | - |
| totalResidues | 24 |
| Quality Control | |
|---|---|
| RMSd | 3.083 (0.717) Å  |
| Rgyr | 13.457 (0.486) Å  |
| SASA | 4506.046 (95.506) Ų  |
| RMSf |  |