Entry: NAFlex_2rn1
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC0 |
| Simulation Date | 2014-Mar-03 |
| Simulated Time | 906 ns |
| Time Step | 10ps |
| Parts | only RNA |
| Temperature | 300K |
| Water | TIP3P |
| Additional Solvent | No |
| Counter Ions | Na+ |
| Ionic Concentration | Electroneutrality |
| Additional Ions | No |
| Additional Molecules | No |
| Ions Parameters | Dang |
Unified Molecular Modeling (UMM) Metadata
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(Click to see full UMM)
| Simulation Metadata (UMM) | |
|---|---|
| AdditionalIons | No |
| AdditionalMolecules | No |
| AdditionalSolvent | No |
| Author | I.F. |
| Chains | ssRNA |
| Comments | kissing loop |
| CounterIons | Na+ |
| Format | mdcrd |
| FrameStep | 10ps |
| Frames | 90625 |
| IonicConcentration | Electroneutrality |
| IonsParameters | Dang |
| Ligands | No |
| NucType | RNA |
| PDB | 2RN1 |
| Parts | only RNA |
| RMSd_avg | 2.063 |
| RMSd_stdev | 0.324 |
| Rgyr_avg | 0.000 |
| Rgyr_stdev | 0.000 |
| SASA_avg | 0.000 |
| SASA_stdev | 0.000 |
| SubType | A |
| Temperature | 300K |
| Topology | 2rn1.vac.top |
| Trajectory | 2rn1.dry.trj.gz |
| Water | TIP3P |
| _id | NAFlex_2rn1 |
| altPDB | 1KIS 2RN1 |
| 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 | 2014-Mar-03 |
| description | RNA-A Naked ParmBSC0 TIP3P Electroneutral TAR Hairpin-loops Aptamer Kissing-loops |
| forceField | parmBSC0 |
| ionsModel | - |
| moleculeType | Rna |
| rev_sequence | GCUGGUCCCAGACAGC |
| saltConcentration | - |
| sequence | GAGCCCUGGGAGGCUC |
| soluteAtoms | 1032 |
| soluteCharge | -30 |
| soluteResidues | 32 |
| solventAtoms | - |
| solventResidues | - |
| time | 906 |
| totalAtoms | 1032 |
| totalCharge | -30 |
| totalIons | - |
| totalResidues | 32 |
| Quality Control | |
|---|---|
| RMSd | 2.063 (0.324) Å  |
| Rgyr |  |
| SASA |  |
| RMSf |  |
