Entry: NAFlex_FOXO3_crystal_rep5
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 2018-Dec-21 |
| Simulated Time | 50 ns |
| Time Step | 10 ps |
| Parts | DNA+protein+ions |
| 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 | 2UZK |
| Parts | DNA+protein+ions |
| RMSd_avg | 2.221 |
| RMSd_stdev | 0.293 |
| Rgyr_avg | 17.396 |
| Rgyr_stdev | 0.269 |
| SASA_avg | 11413.190 |
| SASA_stdev | 258.589 |
| SubType | B |
| Temperature | 300K |
| Topology | FOXO3_orig_minim_nowater.gro |
| Trajectory | FOXO3_rep5_mdprod_sample.xtc |
| Water | SPCE |
| _id | NAFlex_FOXO3_crystal_rep5 |
| dataset | Array |
| date | 2018-Dec-21 |
| description | DNA-B Duplex Protein-Nuc SPC/E AddedSalt |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | GCGTTGTTTACATAGTC |
| saltConcentration | - |
| sequence | GACTATGTAAACAACGC |
| soluteAtoms | 2620 |
| soluteCharge | - |
| soluteResidues | 131 |
| solventAtoms | - |
| solventResidues | - |
| time | 50 |
| totalAtoms | 2620 |
| totalCharge | - |
| totalIons | - |
| totalResidues | 131 |
| Quality Control | |
|---|---|
| RMSd | 2.221 (0.293) Å  |
| Rgyr | 17.396 (0.269) Å  |
| SASA | 11413.190 (258.589) Ų  |
| RMSf |  |
