Entry: NAFlex_RNA_miniABC_KCl_8
Nucleic Acid Data:
| Sequence | GCGGAGGGCCGGGUGGGC |
| Rev. Sequence | GCCCACCCGGCCCUCCGC |
| Type | RNA |
| SubType | A |
| Chains | duplex |
| Pdb | - |
| Ligands | No |
| Keywords | RNA-A Duplex Naked TIP3P AddedSalt |
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC0+OL3 |
| Simulation Date | 2022-Sep-05 |
| Simulated Time | 1,000 ns |
| Time Step | 20 ps |
| Parts | RNA+ions |
| Temperature | 298K |
| Water | TIP3P |
| Additional Solvent | No |
| Counter Ions | K+ |
| Ionic Concentration | 0.15 M |
| Additional Ions | KCl |
| 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 | KCl |
| AdditionalMolecules | No |
| AdditionalSolvent | No |
| Author | A.H. |
| Chains | duplex |
| Comments | miniABC project, RNA collection |
| CounterIons | K+ |
| Format | nc |
| FrameStep | 20 ps |
| Frames | 1000000 |
| IonicConcentration | 0.15 M |
| IonsParameters | Dang |
| Ligands | No |
| NucType | RNA |
| PDB | NONE |
| Parts | RNA+ions |
| RMSd_avg | 2.937 |
| RMSd_stdev | 0.657 |
| Rgyr_avg | 16.773 |
| Rgyr_stdev | 0.547 |
| SASA_avg | 6606.704 |
| SASA_stdev | 100.081 |
| SubType | A |
| Temperature | 298K |
| Topology | GCGGAGGGCCGGGUGGGC.dry.parmtop |
| Trajectory | GCGGAGGGCCGGGUGGGC.dry.5000.nc |
| Water | TIP3P |
| _id | NAFlex_RNA_miniABC_KCl_8 |
| boxAngle | 109.471219 |
| boxX | 82.550182 |
| boxY | 82.550182 |
| boxZ | 82.550182 |
| dataset | Array |
| date | 2022-Sep-05 |
| description | RNA-A Duplex Naked TIP3P AddedSalt |
| forceField | parmBSC0+OL3 |
| ionsModel | - |
| moleculeType | Rna |
| rev_sequence | GCCCACCCGGCCCUCCGC |
| saltConcentration | - |
| sequence | GCGGAGGGCCGGGUGGGC |
| soluteAtoms | 1164 |
| soluteCharge | -34 |
| soluteResidues | 36 |
| solventAtoms | - |
| solventResidues | - |
| time | 1,000 |
| totalAtoms | 1164 |
| totalCharge | -34 |
| totalIons | - |
| totalResidues | 36 |
| Quality Control | |
|---|---|
| RMSd | 2.937 (0.657) Å  |
| Rgyr | 16.773 (0.547) Å  |
| SASA | 6606.704 (100.081) Ų  |
| RMSf |  |
