Entry: NAFlex_437d
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC0 |
| Simulation Date | 2015-Apr-25 |
| Simulated Time | 1,015 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 | single |
| Comments | pseudoknot |
| CounterIons | Na+ |
| Format | mdcrd |
| FrameStep | 10ps |
| Frames | 101506 |
| IonicConcentration | Electroneutrality |
| IonsParameters | Dang |
| Ligands | No |
| NucType | RNA |
| PDB | 437D |
| Parts | only RNA |
| RMSd_avg | 3.893 |
| RMSd_stdev | 0.414 |
| Rgyr_avg | 12.321 |
| Rgyr_stdev | 0.301 |
| SASA_avg | 4482.699 |
| SASA_stdev | 109.277 |
| SubType | A |
| Temperature | 300K |
| Topology | pseudoknot.vac.top |
| Trajectory | pseudoknot.dry.trj.gz |
| Water | TIP3P |
| _id | NAFlex_437d |
| altPDB | 1L2X 1L3D 437D |
| 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 | RNA-A Single Stranded Naked ParmBSC0 TIP3P Electroneutral Pseudoknot Flipout-bases Overhanging-bases Loops |
| forceField | parmBSC0 |
| ionsModel | - |
| moleculeType | Rna |
| rev_sequence | - |
| saltConcentration | - |
| sequence | GGCGCGGCACCGUCCGCGGAACAAACGG |
| soluteAtoms | 911 |
| soluteCharge | -27 |
| soluteResidues | 28 |
| solventAtoms | - |
| solventResidues | - |
| time | 1,015 |
| totalAtoms | 911 |
| totalCharge | -27 |
| totalIons | - |
| totalResidues | 28 |
| Quality Control | |
|---|---|
| RMSd | 3.893 (0.414) Å  |
| Rgyr | 12.321 (0.301) Å  |
| SASA | 4482.699 (109.277) Ų  |
| RMSf |  |
