Entry: NAFlex_DTipDang015M_CG


Nucleic Acid Data:


SequenceCGCGAATTCGCG
Rev. SequenceCGCGAATTCGCG
TypeDNA
SubTypeB
Chainsduplex
Pdb-
LigandsNo
KeywordsDNA-B Duplex Naked


Simulation Metadata
Force FieldCGeNArate
Simulation Date2024-Jul-08
Simulated Time1,000 ns
Time Step20 ps
PartsDNA
Temperature298K
WaterNo
Additional SolventNo
Counter IonsNo
Ionic ConcentrationNo
Additional IonsNo
Additional MoleculesNo
Ions ParametersNo
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
Simulation Metadata (UMM)
AdditionalIonsNo
AdditionalMoleculesNo
AdditionalSolventNo
AuthorD.F.
Chainsduplex
CommentsCGeNArate: A Sequence-Dependent Coarse-Grained Model of DNA for Accurate Atomistic MD Simulations of kb-long Duplexes, DOI: 10.1093/nar/gkae444
CounterIonsNo
Formatmdcrd
FrameStep20 ps
Frames50000
IonicConcentrationNo
IonsParametersNo
LigandsNo
NucTypeDNA
PDBNONE
PartsDNA
RMSd_avg1.640
RMSd_stdev0.252
Rgyr_avg13.431
Rgyr_stdev0.259
SASA_avg2124.390
SASA_stdev12.985
SubTypeB
Temperature298K
TopologyDTipDang015MStripped.pdb
TrajectoryDTipDang015Maligned.mdcrd
WaterNo
_idNAFlex_DTipDang015M_CG
datasetArray
date2024-Jul-08
descriptionDNA-B Duplex Naked
forceFieldCGeNArate
ionsModel-
moleculeTypeDna
rev_sequenceCGCGAATTCGCG
saltConcentration-
sequenceCGCGAATTCGCG
soluteAtoms24
soluteCharge-
soluteResidues24
solventAtoms-
solventResidues-
time1,000
totalAtoms24
totalCharge-
totalIons-
totalResidues24
Quality Control
RMSd1.640 (0.252) Å    
Rgyr13.431 (0.259) Å    
SASA2124.390 (12.985) Ų    
RMSf