| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 2015-04-26 |
| 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 | 1P71 |
| Parts | DNA+protein+ions |
| RMSd_avg | 4.034 |
| RMSd_stdev | 0.648 |
| Rgyr_avg | 20.528 |
| Rgyr_stdev | 0.560 |
| SASA_avg | 7027.909 |
| SASA_stdev | 116.249 |
| SubType | B |
| Temperature | 298K |
| Topology | f1p71A_nowat.prmtop |
| Trajectory | f1p71A_nowat.nc |
| Water | SPCE |
| _id | NAFlex_1p71 |
| altPDB | 1P71 4QJU |
| 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 | 2015-04-26 |
| description | DNA-B Duplex Complex ParmBSC1 SPC/E AddedSalt Protein-nuc Flipout-bases |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Prot-Dna |
| rev_sequence | TGCTTATCAATTTGTTGCA |
| saltConcentration | - |
| sequence | TGCTTATCAATTTGTTGCA |
| soluteAtoms | 4090 |
| soluteCharge | -28 |
| soluteResidues | 225 |
| solventAtoms | - |
| solventResidues | - |
| time | 1,000 |
| totalAtoms | 4090 |
| totalCharge | -28 |
| totalIons | - |
| totalResidues | 225 |
| Quality Control | |
|---|---|
| RMSd | - |
| Rgyr | - |
| SASA | - |
| RMSf | - |