Entry: NAFlex_gcf1p_2pro_2dna
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 2022-Aug-01 |
| Simulated Time | 200 ns |
| Time Step | 1 ps |
| Parts | Prot,DNA |
| Temperature | 300K |
| Water | TIP3P |
| Additional Solvent | No |
| Counter Ions | K+,Cl- |
| 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 | F.B. |
| Chains | duplex |
| Comments | gcf1p project |
| CounterIons | K+,Cl- |
| Format | netcdf |
| FrameStep | 1 ps |
| Frames | 48000 |
| IonicConcentration | Electroneutrality |
| IonsParameters | Dang |
| Ligands | No |
| NucType | Prot-DNA |
| PDB | 1PRO |
| Parts | Prot,DNA |
| RMSd_avg | 5.948 |
| RMSd_stdev | 0.866 |
| Rgyr_avg | 37.516 |
| Rgyr_stdev | 0.587 |
| SASA_avg | 43606.923 |
| SASA_stdev | 1104.158 |
| SubType | B |
| Temperature | 300K |
| Topology | 1pro_1longDNA_nowat.prmtop |
| Trajectory | 1pro_1longDNA_500reimage.nc |
| Water | TIP3P |
| _id | NAFlex_gcf1p_2pro_2dna |
| dataset | Array |
| date | 2022-Aug-01 |
| description | -B Duplex Naked TIP3P Electroneutral |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Prot-Dna |
| rev_sequence | TATTATATAATTTATTAT|ATAATAAATTATATAATATAATATATATATATATA |
| saltConcentration | - |
| sequence | ATAATAAATTATATAATATAATATATATATATATA | TATATATATATATATTA |
| sequenceMulti | Array |
| soluteAtoms | 10806 |
| soluteCharge | -112 |
| soluteResidues | 516 |
| solventAtoms | - |
| solventResidues | - |
| time | 200 |
| totalAtoms | 10806 |
| totalCharge | -112 |
| totalIons | - |
| totalResidues | 516 |
| Quality Control | |
|---|---|
| RMSd | 5.948 (0.866) Å  |
| Rgyr | 37.516 (0.587) Å  |
| SASA | 43606.923 (1104.158) Ų  |
| RMSf |  |