Simulation Metadata (UMM) |
AdditionalIons | KCl |
AdditionalMolecules | No |
AdditionalSolvent | No |
Author | P.D. |
Chains | duplex |
Comments | 700 ns of MD simulation of a WT 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 | 2.079 |
RMSd_stdev | 0.182 |
Rgyr_avg | 45.012 |
Rgyr_stdev | 0.547 |
SASA_avg | 50458.515 |
SASA_stdev | 612.524 |
SubType | B |
Temperature | 300K |
Topology | nucWT_dry.top |
Trajectory | nucWT_dry.trj.gz |
Water | TIP3P |
_id | NAFlex_nucWT16 |
dataset | Array |
date | 0.00000000 1536537600 |
description | DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
forceField | parmBSC1 |
ionsModel | - |
moleculeType | Dna |
rev_sequence | ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGATTCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT |
saltConcentration | - |
sequence | ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGAATCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT |
soluteAtoms | 9346 |
soluteCharge | -292 |
soluteResidues | 294 |
solventAtoms | - |
solventResidues | - |
time | 700 |
totalAtoms | 9346 |
totalCharge | -292 |
totalIons | - |
totalResidues | 294 |