Entry: NAFlex_DDD_bsc1
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC0 |
| Simulation Date | 2015-Aug-06 |
| Simulated Time | 10,000 ns |
| Time Step | 20 ps |
| Parts | DNA+ions |
| Temperature | 298K |
| Water | TIP3P |
| Additional Solvent | No |
| Counter Ions | Na+ |
| Ionic Concentration | Electroneutrality |
| 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 | - |
| CounterIons | Na+ |
| Format | netcdf |
| FrameStep | 20 ps |
| Frames | 500000 |
| IonicConcentration | Electroneutrality |
| IonsParameters | Dang |
| Ligands | No |
| NucType | DNA |
| PDB | 1NAJ |
| Parts | DNA+ions |
| RMSd_avg | 1.734 |
| RMSd_stdev | 0.368 |
| Rgyr_avg | 13.268 |
| Rgyr_stdev | 0.274 |
| SASA_avg | 4360.452 |
| SASA_stdev | 72.809 |
| SubType | B |
| Temperature | 298K |
| Topology | DDD10micros_nowat.prmtop |
| Trajectory | DDD10micros_nowat.nc |
| Water | TIP3P |
| _id | NAFlex_DDD_bsc1 |
| dataset | Array |
| date | 2015-Aug-06 |
| description | DNA-B Duplex Naked DDD ParmBSC0 TIP3P Electroneutral |
| forceField | parmBSC0 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | CGCGAATTCGCG |
| saltConcentration | - |
| sequence | CGCGAATTCGCG |
| soluteAtoms | 758 |
| soluteCharge | -22 |
| soluteResidues | 24 |
| solventAtoms | - |
| solventResidues | - |
| time | 10,000 |
| totalAtoms | 758 |
| totalCharge | -22 |
| totalIons | - |
| totalResidues | 24 |
| Quality Control | |
|---|---|
| RMSd | 1.734 (0.368) Å  |
| Rgyr | 13.268 (0.274) Å  |
| SASA | 4360.452 (72.809) Ų  |
| RMSf |  |
