Entry: NAFlex_GC-rich_Lys_1500mM
Nucleic Acid Data:
| Sequence | GTCCACGCCC |
| Rev. Sequence | GGTGCGACGG |
| Type | DNA |
| SubType | B |
| Chains | duplex |
| Pdb | - |
| Ligands | No |
| Keywords | DNA-B Duplex Naked SPC/E AddedSalt |
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 2021-Nov-25 |
| Simulated Time | 400 ns |
| Time Step | 1 ps |
| Parts | DNA+ions |
| Temperature | 298K |
| Water | SPCE |
| Additional Solvent | No |
| Counter Ions | K+Cl- |
| Ionic Concentration | 1.5M |
| Additional Ions | Lys |
| 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 | Lys |
| AdditionalMolecules | No |
| AdditionalSolvent | No |
| Author | F.B. |
| Chains | duplex |
| Comments | LysArg project |
| CounterIons | K+Cl- |
| Format | mdcrd |
| FrameStep | 1 ps |
| Frames | 400000 |
| IonicConcentration | 1.5M |
| IonsParameters | Dang |
| Ligands | No |
| NucType | DNA |
| PDB | NONE |
| Parts | DNA+ions |
| RMSd_avg | 3.361 |
| RMSd_stdev | 0.725 |
| Rgyr_avg | 20.192 |
| Rgyr_stdev | 0.471 |
| SASA_avg | 7067.483 |
| SASA_stdev | 145.394 |
| SubType | B |
| Temperature | 298K |
| Topology | mdp_first_frame_nowat_tleap.top |
| Trajectory | traj_nowat.trj |
| Water | SPCE |
| _id | NAFlex_GC-rich_Lys_1500mM |
| dataset | Array |
| date | 2021-Nov-25 |
| description | DNA-B Duplex Naked SPC/E AddedSalt |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | GGTGCGACGG |
| saltConcentration | - |
| sequence | GTCCACGCCC |
| soluteAtoms | 1262 |
| soluteCharge | -38 |
| soluteResidues | 40 |
| solventAtoms | - |
| solventResidues | - |
| time | 400 |
| totalAtoms | 1262 |
| totalCharge | -38 |
| totalIons | - |
| totalResidues | 40 |
| Quality Control | |
|---|---|
| RMSd | 3.361 (0.725) Å  |
| Rgyr | 20.192 (0.471) Å  |
| SASA | 7067.483 (145.394) Ų  |
| RMSf |  |