Entry: NAFlex_2nq1
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 2015-Apr-25 |
| 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/2nq1 |
| CounterIons | Na+ |
| Format | mdcrd |
| FrameStep | 1ps |
| Frames | 590000 |
| IonicConcentration | Electroneutrality |
| IonsParameters | Dang |
| Ligands | no |
| NucType | DNA |
| PDB | 2NQ1 |
| Parts | ions + DNA |
| RMSd_avg | 2.454 |
| RMSd_stdev | 0.376 |
| Rgyr_avg | 13.372 |
| Rgyr_stdev | 0.338 |
| SASA_avg | 4316.475 |
| SASA_stdev | 68.559 |
| SubType | B |
| Temperature | 300K |
| Topology | 2nq1.dry.top |
| Trajectory | 2nq1_recenter.trj |
| Water | TIP3P |
| _id | NAFlex_2nq1 |
| altPDB | 1PG9 1PGC 2NPW 2NQ0 2NQ1 2NQ4 |
| 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 | DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | GGAGGCCTGAGG |
| saltConcentration | - |
| sequence | CCTCAGGCCTCC |
| soluteAtoms | 757 |
| soluteCharge | -22 |
| soluteResidues | 24 |
| solventAtoms | - |
| solventResidues | - |
| time | 590 |
| totalAtoms | 757 |
| totalCharge | -22 |
| totalIons | - |
| totalResidues | 24 |
| Quality Control | |
|---|---|
| RMSd | 2.454 (0.376) Å  |
| Rgyr | 13.372 (0.338) Å  |
| SASA | 4316.475 (68.559) Ų  |
| RMSf |  |
