Entry: NAFlex_2hdc
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 1436832000000 |
| Simulated Time | 1,000 |
| Time Step | 1 ps |
| Parts | DNA+protein+ions |
| Temperature | 298K |
| Water | SPCE |
| Additional Solvent | No |
| Counter Ions | K+Cl- |
| Ionic Concentration | 0.15M |
| 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 | F.B. |
| Chains | duplex |
| Comments | - |
| CounterIons | K+Cl- |
| Format | netcdf |
| FrameStep | 1 ps |
| Frames | 1000000 |
| IonicConcentration | 0.15M |
| IonsParameters | Dang |
| Ligands | No |
| NucType | DNA |
| PDB | 1HLV |
| Parts | DNA+protein+ions |
| RMSd_avg | 2.390 |
| RMSd_stdev | 0.524 |
| Rgyr_avg | 17.475 |
| Rgyr_stdev | 0.338 |
| SASA_avg | 6136.608 |
| SASA_stdev | 93.895 |
| SubType | B |
| Temperature | 298K |
| Topology | f2hdc_nowat.prmtop |
| Trajectory | f2hdc_nowat.nc |
| Water | SPCE |
| _id | NAFlex_2hdc |
| boxAngle | 109.471219 |
| boxX | 75.2935821 |
| boxY | 75.2935821 |
| boxZ | 75.2935821 |
| dataset | Array |
| date | 1436832000000 |
| description | DNA-B Duplex Protein-Nuc ParmBSC1 SPC/E AddedSalt |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | GTATTGTTATTTTAAGC |
| saltConcentration | - |
| sequence | GCTTAAAATAACAATAC |
| soluteAtoms | 1082 |
| soluteCharge | -32 |
| soluteResidues | 34 |
| solventAtoms | - |
| solventResidues | - |
| time | 1,000 |
| totalAtoms | 1082 |
| totalCharge | -32 |
| totalIons | - |
| totalResidues | 34 |
| Quality Control | |
|---|---|
| RMSd | 2.390 (0.524) Å  |
| Rgyr | 17.475 (0.338) Å  |
| SASA | 6136.608 (93.895) Ų  |
| RMSf |  |
