| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 0.00000000 1429833600 |
| Simulated Time | 1,000 |
| Time Step | 1 ps |
| Parts | DNA+protein+ions |
| Temperature | 298K |
| Water | SPCE |
| Additional Solvent | No |
| Counter Ions | K+Cl- |
| Ionic Concentration | 0.15M |
| Additional Ions | No |
| Additional Molecules | No |
| Ions Parameters | Dang |
| Simulation Metadata (UMM) | |
|---|---|
| AdditionalIons | No |
| AdditionalMolecules | No |
| AdditionalSolvent | No |
| Author | F.B. |
| Chains | duplex |
| Comments | - |
| CounterIons | K+Cl- |
| Format | netcdf |
| FrameStep | 1 ps |
| Frames | 1000000 |
| IonicConcentration | 0.15M |
| IonsParameters | Dang |
| Ligands | No |
| NucType | DNA |
| PDB | 1TRO |
| Parts | DNA+protein+ions |
| RMSd_avg | 2.411 |
| RMSd_stdev | 0.433 |
| Rgyr_avg | 18.311 |
| Rgyr_stdev | 0.342 |
| SASA_avg | 6451.957 |
| SASA_stdev | 97.661 |
| SubType | B |
| Temperature | 298K |
| Topology | f1tro_nowat.prmtop |
| Trajectory | f1tro_nowat.nc |
| Water | SPCE |
| _id | NAFlex_1tro |
| authors | Ivan Ivani, Pablo D. Dans, Agnès Noy, Alberto Pérez, Ignacio Faustino, Adam Hospital, Jürgen Walther, Pau Andrio, Ramon Goñi, Alexandra Balaceanu, Guillem Portella, Federica Battistini, Josep Lluís Gelpí, Carlos González, Michele Vendruscolo, Charles A. Laughton, Sarah A. Harris, David A. Case and Modesto Orozco |
| dataset | Array |
| date | 0.00000000 1429833600 |
| description | DNA-B Duplex Complex ParmBSC1 SPC/E AddedSalt Prot-nuc Overhanging-bases |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Prot-Dna |
| rev_sequence | GTACTAGTTAACTAGTAC |
| saltConcentration | - |
| sequence | GTACTAGTTAACTAGTAC |
| soluteAtoms | 4445 |
| soluteCharge | -42 |
| soluteResidues | 239 |
| solventAtoms | - |
| solventResidues | - |
| time | 1,000 |
| totalAtoms | 4445 |
| totalCharge | -42 |
| totalIons | - |
| totalResidues | 239 |
| Quality Control | |
|---|---|
| RMSd | - |
| Rgyr | - |
| SASA | - |
| RMSf | - |