Molecular Dynamics Simulation Database for MuG project. Powered by BIGNASim.
User: Anonymous
Entry: NAFlex_MuG_TRF1
MD Simulation >> (Click to expand/shrink)
| Simulation Metadata | |
|---|---|
| Force Field | parmBSC0 |
| Simulation Date | 2016-May-11 |
| Simulated Time | 40 ns |
| Time Step | 1 ps |
| Parts | DNA+ions |
| Temperature | 300K |
| Water | SPCE |
| Additional Solvent | No |
| Counter Ions | Na+ |
| Ionic Concentration | 0.15M |
| 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 | M.P.C.L. |
| Chains | duplex |
| Comments | A Comprehensive Model for the Recognition of Human Telomeres by TRF1 |
| CounterIons | Na+ |
| Format | mdcrd |
| FrameStep | 1 ps |
| Frames | 40000 |
| IonicConcentration | 0.15M |
| IonsParameters | Dang |
| Ligands | No |
| NucType | Prot-DNA |
| PDB | 1W0T |
| Parts | DNA+ions |
| RMSd_avg | 2.531 |
| RMSd_stdev | 0.433 |
| Rgyr_avg | 19.047 |
| Rgyr_stdev | 0.396 |
| SASA_avg | 6630.185 |
| SASA_stdev | 110.995 |
| SubType | B |
| Temperature | 300K |
| Topology | wtrep1nw.top.gz |
| Trajectory | rep1nwdt10.trj.gz |
| Water | SPCE |
| _id | NAFlex_MuG_TRF1 |
| dataset | Array |
| date | 2016-May-11 |
| description | DNA-B Duplex Complex ParmBSC0 SPC/E |
| forceField | parmBSC0 |
| ionsModel | - |
| moleculeType | Dna |
| rev_sequence | CTAACCCTAACCCTAACA |
| saltConcentration | - |
| sequence | TGTTAGGGTTAGGGTTAG |
| soluteAtoms | 1146 |
| soluteCharge | -35 |
| soluteResidues | 36 |
| solventAtoms | - |
| solventResidues | - |
| time | 40 |
| totalAtoms | 1146 |
| totalCharge | -35 |
| totalIons | - |
| totalResidues | 36 |
| Quality Control | |
|---|---|
| RMSd | 2.531 (0.433) Å  |
| Rgyr | 19.047 (0.396) Å  |
| SASA | 6630.185 (110.995) Ų  |
| RMSf |  |
