Entry: NAFlex_1d89
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 2015-Apr-20 |
| Simulated Time | 200 ns |
| Time Step | 1ps |
| Parts | ions + 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 | A.P. |
| Chains | duplex |
| Comments | /orozco/scratch/parmBSC1/Alberto2/1D89 |
| CounterIons | Na+ |
| Format | mdcrd |
| FrameStep | 1ps |
| Frames | 200000 |
| IonicConcentration | Electroneutrality |
| IonsParameters | Dang |
| Ligands | no |
| NucType | DNA |
| PDB | 1D89 |
| Parts | ions + DNA |
| RMSd_avg | 2.178 |
| RMSd_stdev | 0.372 |
| Rgyr_avg | 13.402 |
| Rgyr_stdev | 0.297 |
| SASA_avg | 4376.523 |
| SASA_stdev | 72.855 |
| SubType | B |
| Temperature | 300K |
| Topology | 1D89.dry.top |
| Trajectory | 1D89.trj |
| Water | TIP3P |
| _id | NAFlex_1d89 |
| boxAngle | 109.471219 |
| boxX | 62.7319808 |
| boxY | 62.7319808 |
| boxZ | 62.7319808 |
| dataset | Array |
| date | 2015-Apr-20 |
| description | DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | CGTTTTTTCGCG |
| saltConcentration | - |
| sequence | CGCGAAAAAACG |
| soluteAtoms | 760 |
| soluteCharge | -22 |
| soluteResidues | 24 |
| solventAtoms | - |
| solventResidues | - |
| time | 200 |
| totalAtoms | 760 |
| totalCharge | -22 |
| totalIons | - |
| totalResidues | 24 |
| Quality Control | |
|---|---|
| RMSd | 2.178 (0.372) Å  |
| Rgyr | 13.402 (0.297) Å  |
| SASA | 4376.523 (72.855) Ų  |
| RMSf |  |
