Entry: NAFlex_AT-rich_crowd_Lys_500mM
Nucleic Acid Data:
| Sequence | TGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGT |
| Rev. Sequence | ACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACA |
| Type | DNA |
| SubType | B |
| Chains | Multiple duplex |
| Pdb | - |
| Ligands | No |
| Keywords | DNA-B Duplex Naked TIP3P AddedSalt |
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 2021-Dec-02 |
| Simulated Time | 5,000 ns |
| Time Step | 20 ps |
| Parts | DNA+ions |
| Temperature | 298K |
| Water | TIP3P |
| Additional Solvent | No |
| Counter Ions | Na+Cl- |
| Ionic Concentration | 0.5M |
| Additional Ions | Lys |
| Additional Molecules | No |
| Ions Parameters | Joung&Cheatham |
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
(Click to see full UMM)
| Simulation Metadata (UMM) | |
|---|---|
| AdditionalIons | Lys |
| AdditionalMolecules | No |
| AdditionalSolvent | No |
| Author | F.B. |
| Chains | Multiple duplex |
| Comments | LysArg project |
| CounterIons | Na+Cl- |
| Format | mdcrd |
| FrameStep | 20 ps |
| Frames | 250000 |
| IonicConcentration | 0.5M |
| IonsParameters | Joung&Cheatham |
| Ligands | No |
| NucType | DNA |
| PDB | NONE |
| Parts | DNA+ions |
| RMSd_avg | 109.003 |
| RMSd_stdev | 8.686 |
| Rgyr_avg | 86.196 |
| Rgyr_stdev | 6.791 |
| SASA_avg | 39034.767 |
| SASA_stdev | 2345.153 |
| SubType | B |
| Temperature | 298K |
| Topology | mdp_first_frame_nowat_tleap.top |
| Trajectory | traj_nowat.trj |
| Water | TIP3P |
| _id | NAFlex_AT-rich_crowd_Lys_500mM |
| dataset | Array |
| date | 2021-Dec-02 |
| description | DNA-B Duplex Naked TIP3P AddedSalt |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | ACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACA |
| saltConcentration | - |
| sequence | TGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGT |
| soluteAtoms | 11460 |
| soluteCharge | 11460 |
| soluteResidues | 360 |
| solventAtoms | - |
| solventResidues | - |
| time | 5,000 |
| totalAtoms | 11460 |
| totalCharge | 11460 |
| totalIons | - |
| totalResidues | 360 |
| Quality Control | |
|---|---|
| RMSd | 109.003 (8.686) Å  |
| Rgyr | 86.196 (6.791) Å  |
| SASA | 39034.767 (2345.153) Ų  |
| RMSf |  |