Entry: NAFlex_FOXA3_dna_rep1
Nucleic Acid Data:
| Sequence | GACTAAGTCAACCACGC |
| Rev. Sequence | GCGTGGTTGACTTAGTC |
| Type | DNA |
| SubType | B |
| Chains | duplex |
| Pdb | - |
| Ligands | No |
| Keywords | DNA-B Duplex Naked SPC/E AddedSalt |
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 2019-Jan-11 |
| Simulated Time | 50 ns |
| Time Step | 10 ps |
| Parts | DNA |
| Temperature | 300K |
| Water | SPCE |
| Additional Solvent | No |
| Counter Ions | Na+Cl- |
| Ionic Concentration | 0.05M |
| Additional Ions | No |
| Additional Molecules | No |
| Ions Parameters | - |
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 | A.M. |
| Chains | duplex |
| Comments | N/A |
| CounterIons | Na+Cl- |
| Format | xtc |
| FrameStep | 10 ps |
| Frames | 5000 |
| IonicConcentration | 0.05M |
| IonsParameters | - |
| Ligands | No |
| NucType | DNA |
| PDB | - |
| Parts | DNA |
| RMSd_avg | 2.157 |
| RMSd_stdev | 0.523 |
| Rgyr_avg | 17.469 |
| Rgyr_stdev | 0.345 |
| SASA_avg | 6105.721 |
| SASA_stdev | 94.384 |
| SubType | B |
| Temperature | 300K |
| Topology | FOXA3_dna_minim_nowater.gro |
| Trajectory | FOXA3_dna_rep1_mdprod_sample.xtc |
| Water | SPCE |
| _id | NAFlex_FOXA3_dna_rep1 |
| dataset | Array |
| date | 2019-Jan-11 |
| description | DNA-B Duplex Naked SPC/E AddedSalt |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | GCGTGGTTGACTTAGTC |
| saltConcentration | - |
| sequence | GACTAAGTCAACCACGC |
| soluteAtoms | 1077 |
| soluteCharge | - |
| soluteResidues | 34 |
| solventAtoms | - |
| solventResidues | - |
| time | 50 |
| totalAtoms | 1077 |
| totalCharge | - |
| totalIons | - |
| totalResidues | 34 |
| Quality Control | |
|---|---|
| RMSd | 2.157 (0.523) Å  |
| Rgyr | 17.469 (0.345) Å  |
| SASA | 6105.721 (94.384) Ų  |
| RMSf |  |
