Entry: NAFlex_2hkb
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/2hkb |
| CounterIons | Na+ |
| Format | mdcrd |
| FrameStep | 1ps |
| Frames | 590000 |
| IonicConcentration | Electroneutrality |
| IonsParameters | Dang |
| Ligands | no |
| NucType | DNA |
| PDB | 2HKB |
| Parts | ions + DNA |
| RMSd_avg | 2.593 |
| RMSd_stdev | 0.508 |
| Rgyr_avg | 13.292 |
| Rgyr_stdev | 0.287 |
| SASA_avg | 4330.472 |
| SASA_stdev | 67.966 |
| SubType | B |
| Temperature | 300K |
| Topology | 2hkb.dry.top |
| Trajectory | 2hkb_recenter.trj |
| Water | TIP3P |
| _id | NAFlex_2hkb |
| altPDB | 1AX6 2HKB 2HKC 2MAV 2Z2G 2Z2H |
| 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 | GATGGCGCCGAG |
| saltConcentration | - |
| sequence | CTCGGCGCCATC |
| soluteAtoms | 757 |
| soluteCharge | -22 |
| soluteResidues | 24 |
| solventAtoms | - |
| solventResidues | - |
| time | 590 |
| totalAtoms | 757 |
| totalCharge | -22 |
| totalIons | - |
| totalResidues | 24 |
| Quality Control | |
|---|---|
| RMSd | 2.593 (0.508) Å  |
| Rgyr | 13.292 (0.287) Å  |
| SASA | 4330.472 (67.966) Ų  |
| RMSf |  |
