Entry: NAFlex_1yo5
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 2015-Jul-14 |
| Simulated Time | 1,000 ns |
| 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 |
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 | - |
| CounterIons | K+Cl- |
| Format | netcdf |
| FrameStep | 1 ps |
| Frames | 1000000 |
| IonicConcentration | 0.15M |
| IonsParameters | Dang |
| Ligands | No |
| NucType | DNA |
| PDB | 1YO5 |
| Parts | DNA+protein+ions |
| RMSd_avg | 2.167 |
| RMSd_stdev | 0.488 |
| Rgyr_avg | 13.963 |
| Rgyr_stdev | 0.304 |
| SASA_avg | 4744.831 |
| SASA_stdev | 79.171 |
| SubType | B |
| Temperature | 298K |
| Topology | f1yo5_nowat.prmtop |
| Trajectory | f1yo5_nowat.nc |
| Water | SPCE |
| _id | NAFlex_1yo5 |
| 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 |
| boxAngle | 109.471219 |
| boxX | 65.3586702 |
| boxY | 65.3586702 |
| boxZ | 65.3586702 |
| dataset | Array |
| date | 2015-Jul-14 |
| description | DNA-B Duplex ParmBSC1 SPC/E AddedSalt |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | TAGCAGGATGTGT |
| saltConcentration | - |
| sequence | ACACATCCTGCTA |
| soluteAtoms | 824 |
| soluteCharge | -24 |
| soluteResidues | 26 |
| solventAtoms | - |
| solventResidues | - |
| time | 1,000 |
| totalAtoms | 824 |
| totalCharge | -24 |
| totalIons | - |
| totalResidues | 26 |
| Quality Control | |
|---|---|
| RMSd | 2.167 (0.488) Å  |
| Rgyr | 13.963 (0.304) Å  |
| SASA | 4744.831 (79.171) Ų  |
| RMSf |  |
