Entry: NAFlex_FOXA3_crystal_rep0
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 2018-Dec-17 |
| 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 | Mg2+ |
| Additional Molecules | No |
| Ions Parameters | - |
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
(Click to see full UMM)
| Simulation Metadata (UMM) | |
|---|---|
| AdditionalIons | Mg2+ |
| 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 | 1VTN |
| Parts | DNA+protein+ions |
| RMSd_avg | 1.998 |
| RMSd_stdev | 0.350 |
| Rgyr_avg | 17.326 |
| Rgyr_stdev | 0.267 |
| SASA_avg | 11588.080 |
| SASA_stdev | 283.704 |
| SubType | B |
| Temperature | 300K |
| Topology | FOXA3_rep0_disre_mdprod_step1_nowater.gro |
| Trajectory | FOXA3_rep0_disre_mdprod_sample.xtc |
| Water | SPCE |
| _id | NAFlex_FOXA3_crystal_rep0 |
| dataset | Array |
| date | 2018-Dec-17 |
| description | DNA-B Duplex Protein-Nuc SPC/E AddedSalt |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Prot |
| rev_sequence | GCGTGGTTGACTTAGTC |
| saltConcentration | - |
| sequence | GACTAAGTCAACCACGC |
| soluteAtoms | 2762 |
| soluteCharge | - |
| soluteResidues | 137 |
| solventAtoms | - |
| solventResidues | - |
| time | 50 |
| totalAtoms | 2762 |
| totalCharge | - |
| totalIons | - |
| totalResidues | 137 |
| Quality Control | |
|---|---|
| RMSd | 1.998 (0.350) Å  |
| Rgyr | 17.326 (0.267) Å  |
| SASA | 11588.080 (283.704) Ų  |
| RMSf |  |
