Entry: NAFlex_ProtDNA_1yo5
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 2016-Jan-22 |
| Simulated Time | 2,000 ns |
| 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 |
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 | Prot-DNA study |
| CounterIons | Na+ |
| Format | netcdf |
| FrameStep | 2 ps |
| Frames | 1000000 |
| IonicConcentration | Electroneutrality |
| IonsParameters | Dang |
| Ligands | No |
| NucType | Prot-DNA |
| PDB | 1YO5 |
| Parts | DNA |
| RMSd_avg | 2.167 |
| RMSd_stdev | 0.488 |
| Rgyr_avg | 13.963 |
| Rgyr_stdev | 0.304 |
| SASA_avg | 4744.842 |
| SASA_stdev | 79.178 |
| SubType | B |
| Temperature | 300K |
| Topology | topol.top |
| Trajectory | traj.nc |
| Water | TIP3P |
| _id | NAFlex_ProtDNA_1yo5 |
| boxAngle | 109.471219 |
| boxX | 65.3586702 |
| boxY | 65.3586702 |
| boxZ | 65.3586702 |
| dataset | Array |
| date | 2016-Jan-22 |
| description | DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Prot-Dna |
| rev_sequence | TAGCAGGATGTGT |
| saltConcentration | - |
| sequence | ACACATCCTGCTA |
| soluteAtoms | 824 |
| soluteCharge | -24 |
| soluteResidues | 26 |
| solventAtoms | - |
| solventResidues | - |
| time | 2,000 |
| totalAtoms | 824 |
| totalCharge | -24 |
| totalIons | - |
| totalResidues | 26 |
| Quality Control | |
|---|---|
| RMSd | 2.167 (0.488) Å  |
| Rgyr | 13.963 (0.304) Å  |
| SASA | 4744.842 (79.178) Ų  |
| RMSf |  |
