Entry: NAFlex_HTQ
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 2015-Apr-25 |
| Simulated Time | 1,000 ns |
| Time Step | 2ps |
| Parts | DNA+ions |
| Temperature | 300K |
| Water | TIP3P |
| Additional Solvent | No |
| Counter Ions | K+ |
| 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 | I.I. |
| Chains | quadruplex |
| Comments | - |
| CounterIons | K+ |
| Format | mdcrd |
| FrameStep | 2ps |
| Frames | 500000 |
| IonicConcentration | Electroneutrality |
| IonsParameters | Dang |
| Ligands | No |
| NucType | DNA |
| PDB | 1KF1 |
| Parts | DNA+ions |
| RMSd_avg | 3.659 |
| RMSd_stdev | 0.487 |
| Rgyr_avg | 11.485 |
| Rgyr_stdev | 0.283 |
| SASA_avg | 3766.961 |
| SASA_stdev | 107.267 |
| SubType | G-loop |
| Temperature | 300K |
| Topology | no_wat.top |
| Trajectory | HTQ/with3ions.x.gz |
| Water | TIP3P |
| _id | NAFlex_HTQ |
| altPDB | 143D 1KF1 2E4I 2MCC 2MCO 3R6R 3SC8 3T5E 3UYH 4FXM 4G0F |
| 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-Apr-25 |
| description | DNA Single-Stranded G-Loop Naked ParmBSC1 TIP3P Electroneutral Telomer |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | - |
| saltConcentration | - |
| sequence | AGGGTTAGGGTTAGGGTTAGGG |
| soluteAtoms | 715 |
| soluteCharge | -21 |
| soluteResidues | 22 |
| solventAtoms | - |
| solventResidues | - |
| time | 1,000 |
| totalAtoms | 715 |
| totalCharge | -21 |
| totalIons | - |
| totalResidues | 22 |
| Quality Control | |
|---|---|
| RMSd | 3.659 (0.487) Å  |
| Rgyr | 11.485 (0.283) Å  |
| SASA | 3766.961 (107.267) Ų  |
| RMSf |  |
