Entry: NAFlex_oxyQ
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 | 0.15M |
| Additional Ions | K+Cl- |
| 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 | K+Cl- |
| AdditionalMolecules | No |
| AdditionalSolvent | No |
| Author | I.I. |
| Chains | quadruplex |
| Comments | - |
| CounterIons | K+ |
| Format | mdcrd |
| FrameStep | 2ps |
| Frames | 500000 |
| IonicConcentration | 0.15M |
| IonsParameters | Dang |
| Ligands | No |
| NucType | DNA |
| PDB | 1JRN |
| Parts | DNA+ions |
| RMSd_avg | 0.942 |
| RMSd_stdev | 0.200 |
| Rgyr_avg | 10.189 |
| Rgyr_stdev | 0.154 |
| SASA_avg | 3822.080 |
| SASA_stdev | 65.308 |
| SubType | - |
| Temperature | 300K |
| Topology | withions.top |
| Trajectory | oxyQ/naked.trj.gz |
| Water | TIP3P |
| _id | NAFlex_oxyQ |
| altPDB | 156D 1D59 1JB7 1JRN 1K4X 1L1H 1OTC 1PA6 1QDI 1QDK 2AKG 2GWE 2GWQ 2HBN 2WCN 3EM2 3EQW 3ERU 3ES0 3ET8 3EUI 3EUM 3NYP 3NZ7 4R45 4R47 |
| 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 Quadruplex Naked ParmBSC1 TIP3P AddedSalt Loop Telomer |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | GGGGTTTTGGGG |
| saltConcentration | - |
| sequence | GGGGTTTTGGGG |
| soluteAtoms | 782 |
| soluteCharge | -22 |
| soluteResidues | 24 |
| solventAtoms | - |
| solventResidues | - |
| time | 1,000 |
| totalAtoms | 782 |
| totalCharge | -22 |
| totalIons | - |
| totalResidues | 24 |
| Quality Control | |
|---|---|
| RMSd | 0.942 (0.200) Å  |
| Rgyr | 10.189 (0.154) Å  |
| SASA | 3822.080 (65.308) Ų  |
| RMSf |  |
