Entry: NAFlex_QPS
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC1 |
| Simulation Date | 2015-Apr-29 |
| Simulated Time | 440 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 | quadruplex |
| Comments | /orozco/scratch/parmBSC1/Alberto2/QmanuPS |
| CounterIons | Na+ |
| Format | mdcrd |
| FrameStep | 1ps |
| Frames | 440000 |
| IonicConcentration | Electroneutrality |
| IonsParameters | Dang |
| Ligands | no |
| NucType | DNA |
| PDB | 352D |
| Parts | ions + DNA |
| RMSd_avg | 2.010 |
| RMSd_stdev | 0.135 |
| Rgyr_avg | 8.866 |
| Rgyr_stdev | 0.151 |
| SASA_avg | 2668.707 |
| SASA_stdev | 82.178 |
| SubType | parallel quadruplex |
| Temperature | 300K |
| Topology | QmanuPS.dry.top |
| Trajectory | QmanuPS.trj.gz |
| Water | TIP3P |
| _id | NAFlex_QPS |
| altPDB | 1O0K 1S45 1S47 244D 2CHJ 2CHK 2GW0 2JT7 2KVY 2O4F 352D 4R44 |
| 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 |
| boxAngle | 109.471219 |
| boxX | 68.4799676 |
| boxY | 68.4799676 |
| boxZ | 68.4799676 |
| dataset | Array |
| date | 2015-Apr-29 |
| description | DNA Quadruplex Naked ParmBSC1 TIP3P Electroneutral Parallel |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Dna |
| rev-sequence | - |
| rev_sequence | GGGG |
| saltConcentration | - |
| sequence | GGGG | GGGG | GGGG | GGGG |
| sequenceMulti | Array |
| soluteAtoms | 524 |
| soluteCharge | -12 |
| soluteResidues | 16 |
| solventAtoms | - |
| solventResidues | - |
| time | 440 |
| totalAtoms | 524 |
| totalCharge | -12 |
| totalIons | - |
| totalResidues | 16 |
| Quality Control | |
|---|---|
| RMSd | 2.010 (0.135) Å  |
| Rgyr | 8.866 (0.151) Å  |
| SASA | 2668.707 (82.178) Ų  |
| RMSf |  |
