Entry: NAFlex_1vt5
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 2015-Apr-25 |
| Simulated Time | 200 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 | /orozco/scratch/parmBSC1/Alberto2/1vt5 |
| CounterIons | Na+ |
| Format | mdcrd |
| FrameStep | 1ps |
| Frames | 200000 |
| IonicConcentration | Electroneutrality |
| IonsParameters | Dang |
| Ligands | no |
| NucType | DNA |
| PDB | 1VT5 |
| Parts | ions + DNA |
| RMSd_avg | 2.712 |
| RMSd_stdev | 0.457 |
| Rgyr_avg | 10.277 |
| Rgyr_stdev | 0.245 |
| SASA_avg | 2968.466 |
| SASA_stdev | 57.231 |
| SubType | A |
| Temperature | 300K |
| Topology | 1vt5.dry.top |
| Trajectory | 1vt5.trj |
| Water | TIP3P |
| _id | NAFlex_1vt5 |
| altPDB | 187D 1RXA 1RXB 1VT5 259D 2A0P |
| 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-A Duplex Naked ParmBSC1 TIP3P Electroneutral |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | CCCCGGGG |
| saltConcentration | - |
| sequence | CCCCGGGG |
| soluteAtoms | 502 |
| soluteCharge | -14 |
| soluteResidues | 16 |
| solventAtoms | - |
| solventResidues | - |
| time | 200 |
| totalAtoms | 502 |
| totalCharge | -14 |
| totalIons | - |
| totalResidues | 16 |
| Quality Control | |
|---|---|
| RMSd | 2.712 (0.457) Å  |
| Rgyr | 10.277 (0.245) Å  |
| SASA | 2968.466 (57.231) Ų  |
| RMSf |  |
