Entry: NAFlex_2k0v
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 2015-Apr-20 |
| Simulated Time | 590 ns |
| Time Step | 1ps |
| Parts | ions + DNA |
| 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
(Click to see full UMM)
(Click to see full UMM)
| Simulation Metadata (UMM) | |
|---|---|
| AdditionalIons | No |
| AdditionalMolecules | no |
| AdditionalSolvent | No |
| Author | A.P. |
| Chains | duplex |
| Comments | /gpfs/projects/bsc51/bsc51110/BSC1/300_NMR_DATA/2k0v |
| CounterIons | Na+ |
| Format | mdcrd |
| FrameStep | 1ps |
| Frames | 590000 |
| IonicConcentration | Electroneutrality |
| IonsParameters | Dang |
| Ligands | no |
| NucType | DNA |
| PDB | 2K0V |
| Parts | ions + DNA |
| RMSd_avg | 2.042 |
| RMSd_stdev | 0.331 |
| Rgyr_avg | 13.353 |
| Rgyr_stdev | 0.302 |
| SASA_avg | 4334.776 |
| SASA_stdev | 68.627 |
| SubType | B |
| Temperature | 300K |
| Topology | 2k0v.dry.top |
| Trajectory | 2k0v_recenter.trj |
| Water | TIP3P |
| _id | NAFlex_2k0v |
| altPDB | 1A84 1AIO 1IHH 1LU5 2K0T 2K0U 2K0V 3LPV |
| 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-20 |
| description | DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | GGAGACCAGAGG |
| saltConcentration | - |
| sequence | CCTCTGGTCTCC |
| soluteAtoms | 758 |
| soluteCharge | -22 |
| soluteResidues | 24 |
| solventAtoms | - |
| solventResidues | - |
| time | 590 |
| totalAtoms | 758 |
| totalCharge | -22 |
| totalIons | - |
| totalResidues | 24 |
| Quality Control | |
|---|---|
| RMSd | 2.042 (0.331) Å  |
| Rgyr | 13.353 (0.302) Å  |
| SASA | 4334.776 (68.627) Ų  |
| RMSf |  |
