Entry: NAFlex_GAGA_RNA
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 1429920000000 |
| Simulated Time | 1,022 |
| 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 | GAGA TL |
| CounterIons | Na+ |
| Format | mdcrd |
| FrameStep | 10ps |
| Frames | 102257 |
| IonicConcentration | Electroneutrality |
| IonsParameters | Dang |
| Ligands | No |
| NucType | RNA |
| PDB | 1Q9A |
| Parts | only RNA |
| RMSd_avg | 0.874 |
| RMSd_stdev | 0.200 |
| Rgyr_avg | 8.245 |
| Rgyr_stdev | 0.169 |
| SASA_avg | 1969.080 |
| SASA_stdev | 36.240 |
| SubType | A |
| Temperature | 300K |
| Topology | gaga.vac.top |
| Trajectory | gaga.alldry.trj.gz |
| Water | TIP3P |
| _id | NAFlex_GAGA_RNA |
| altPDB | 1Q9A 3DVZ 3DW4 3DW5 3DW6 3DW7 480D 483D |
| 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 | 1429920000000 |
| description | RNA-A Single Stranded Naked ParmBSC0 TIP3P Electroneutral Sarcin-Ricin Hairpin loop Flipout-bases |
| forceField | parmBSC0 |
| ionsModel | - |
| moleculeType | Rna |
| rev_sequence | - |
| saltConcentration | - |
| sequence | CGCGAGAGCG |
| soluteAtoms | 328 |
| soluteCharge | -9 |
| soluteResidues | 10 |
| solventAtoms | - |
| solventResidues | - |
| time | 1,022 |
| totalAtoms | 328 |
| totalCharge | -9 |
| totalIons | - |
| totalResidues | 10 |
| Quality Control | |
|---|---|
| RMSd | 0.874 (0.200) Å  |
| Rgyr | 8.245 (0.169) Å  |
| SASA | 1969.080 (36.240) Ų  |
| RMSf |  |
