| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 0.00000000 1484524800 |
| Simulated Time | 2,000 |
| Time Step | 2 ps |
| Parts | DNA |
| Temperature | 300K |
| Water | TIP3P |
| Additional Solvent | No |
| Counter Ions | Na+ |
| Ionic Concentration | Electroneutrality |
| Additional Ions | No |
| Additional Molecules | No |
| Ions Parameters | Dang |
| Simulation Metadata (UMM) | |
|---|---|
| AdditionalIons | No |
| AdditionalMolecules | No |
| AdditionalSolvent | No |
| Author | P.D. |
| Chains | duplex |
| Comments | Prot-DNA study |
| CounterIons | Na+ |
| Format | netcdf |
| FrameStep | 2 ps |
| Frames | 1000000 |
| IonicConcentration | Electroneutrality |
| IonsParameters | Dang |
| Ligands | No |
| NucType | Prot-DNA |
| PDB | 1J46 |
| Parts | DNA |
| RMSd_avg | 2.191 |
| RMSd_stdev | 0.368 |
| Rgyr_avg | 14.943 |
| Rgyr_stdev | 0.316 |
| SASA_avg | 5041.924 |
| SASA_stdev | 78.572 |
| SubType | B |
| Temperature | 300K |
| Topology | topol.top |
| Trajectory | traj.nc |
| Water | TIP3P |
| _id | NAFlex_ProtDNA_1j46 |
| boxAngle | 109.471219 |
| boxX | 68.2816825 |
| boxY | 68.2816825 |
| boxZ | 68.2816825 |
| dataset | Array |
| date | 0.00000000 1484524800 |
| description | DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Prot-Dna |
| rev_sequence | GGTGTTTGTGCAGG |
| saltConcentration | - |
| sequence | CCTGCACAAACACC |
| soluteAtoms | 886 |
| soluteCharge | -26 |
| soluteResidues | 28 |
| solventAtoms | - |
| solventResidues | - |
| time | 2,000 |
| totalAtoms | 886 |
| totalCharge | -26 |
| totalIons | - |
| totalResidues | 28 |
| Quality Control | |
|---|---|
| RMSd | - |
| Rgyr | - |
| SASA | - |
| RMSf | - |