Entry: NAFlex_CTAG_14
Nucleic Acid Data:
| Sequence | CGTCTACTAGTGAGGC |
| Rev. Sequence | GCCTCACTAGTAGACG |
| Type | DNA |
| SubType | B |
| Chains | duplex |
| Pdb | - |
| Ligands | No |
| Keywords | DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 2015-May-27 |
| Simulated Time | 500 ns |
| Time Step | 1 ps |
| Parts | DNA+ions |
| Temperature | 298K |
| Water | TIP3P |
| 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 | A.B. |
| Chains | duplex |
| Comments | - |
| CounterIons | K+Cl- |
| Format | netcdf |
| FrameStep | 1 ps |
| Frames | 500000 |
| IonicConcentration | 0.15M |
| IonsParameters | Dang |
| Ligands | No |
| NucType | DNA |
| PDB | NONE |
| Parts | DNA+ions |
| RMSd_avg | 2.279 |
| RMSd_stdev | 0.498 |
| Rgyr_avg | 16.597 |
| Rgyr_stdev | 0.344 |
| SASA_avg | 5709.513 |
| SASA_stdev | 87.604 |
| SubType | B |
| Temperature | 298K |
| Topology | CTAG_14_nowat.top |
| Trajectory | CTAG_14_nowatReim.nc |
| Water | TIP3P |
| _id | NAFlex_CTAG_14 |
| dataset | Array |
| date | 2015-May-27 |
| description | DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | GCCTCACTAGTAGACG |
| saltConcentration | - |
| sequence | CGTCTACTAGTGAGGC |
| soluteAtoms | 1013 |
| soluteCharge | -30 |
| soluteResidues | 32 |
| solventAtoms | - |
| solventResidues | - |
| time | 500 |
| totalAtoms | 1013 |
| totalCharge | -30 |
| totalIons | - |
| totalResidues | 32 |
| Quality Control | |
|---|---|
| RMSd | 2.279 (0.498) Å  |
| Rgyr | 16.597 (0.344) Å  |
| SASA | 5709.513 (87.604) Ų  |
| RMSf |  |
