Simulation Metadata (UMM) |
Author | Pablo Dans |
AdditionalIons | KCl |
AdditionalMolecules | No |
AdditionalSolvent | No |
Author | . |
Chains | duplex |
Comments | 700 ns of MD simulation of a modified H3S57p nucleosome. |
CounterIons | K+ |
Format | mdcrd |
FrameStep | 100 ps |
Frames | 7000 |
IonicConcentration | 0.15 M |
IonsParameters | Dang |
Ligands | Protein |
NucType | DNA |
PDB | 1KX5 |
Parts | DNA, nucleosome core particle |
RMSd_avg | 2.187 |
RMSd_stdev | 0.250 |
Rgyr_avg | 45.042 |
Rgyr_stdev | 0.549 |
SASA_avg | 51013.972 |
SASA_stdev | 622.825 |
SubType | B |
Temperature | 300K |
Topology | H3S57p_dry.top |
Trajectory | H3S57p_dry.trj.gz |
Water | TIP3P |
_id | NAFlex_H3S57p16 |
dataset | Array |
date | 2018-Sep-10 |
description | DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
forceField | parmBSC1 |
ionsModel | - |
moleculeType | Dna |
rev_sequence | XX |
saltConcentration | - |
sequence | ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGAATCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT | ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGATTCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT |
sequenceMulti | Array |
soluteAtoms | 9374 |
soluteCharge | -296 |
soluteResidues | 296 |
solventAtoms | - |
solventResidues | - |
time | 700 |
totalAtoms | 9374 |
totalCharge | -296 |
totalIons | - |
totalResidues | 296 |