Entry: NAFlex_muAGAG
Nucleic Acid Data:
| Sequence | GCAGAGAGAGAGAGAGGC |
| Rev. Sequence | GCCTCTCTCTCTCTCTGC |
| Type | DNA |
| SubType | B |
| Chains | duplex |
| Pdb | - |
| Ligands | No |
| Keywords | DNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt |
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC0 |
| Simulation Date | 2016-May-04 |
| Simulated Time | 1,000 ns |
| Time Step | 1 ps |
| Parts | DNA+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 | P.D. |
| Chains | duplex |
| Comments | muABC |
| CounterIons | K+Cl- |
| Format | mdcrd |
| FrameStep | 1 ps |
| Frames | 1000000 |
| IonicConcentration | 0.15M |
| IonsParameters | Dang |
| Ligands | No |
| NucType | DNA |
| PDB | NONE |
| Parts | DNA+ions |
| RMSd_avg | 2.968 |
| RMSd_stdev | 0.757 |
| Rgyr_avg | 18.230 |
| Rgyr_stdev | 0.425 |
| SASA_avg | 6435.273 |
| SASA_stdev | 97.802 |
| SubType | B |
| Temperature | 298K |
| Topology | TCGA_nowat.prmtop |
| Trajectory | TCGA_last250ns.trj |
| Water | SPCE |
| _id | NAFlex_muAGAG |
| boxAngle | 109.471219 |
| boxX | 80.6899552 |
| boxY | 80.6899552 |
| boxZ | 80.6899552 |
| dataset | Array |
| date | 2016-May-04 |
| description | DNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt |
| forceField | parmBSC0 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | GCCTCTCTCTCTCTCTGC |
| saltConcentration | - |
| sequence | GCAGAGAGAGAGAGAGGC |
| soluteAtoms | 1139 |
| soluteCharge | -34 |
| soluteResidues | 36 |
| solventAtoms | - |
| solventResidues | - |
| time | 1,000 |
| totalAtoms | 1139 |
| totalCharge | -34 |
| totalIons | - |
| totalResidues | 36 |
| Quality Control | |
|---|---|
| RMSd | 2.968 (0.757) Å  |
| Rgyr | 18.230 (0.425) Å  |
| SASA | 6435.273 (97.802) Ų  |
| RMSf |  |
