Entry: NAFlex_2lef_CG


Nucleic Acid Data:


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


Simulation Metadata
Force FieldCGeNArate
Simulation Date2024-Jul-05
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_avg5.448
RMSd_stdev0.664
Rgyr_avg15.945
Rgyr_stdev0.357
SASA_avg2667.139
SASA_stdev15.056
SubTypeB
Temperature298K
Topology2lefStripped.pdb
Trajectory2lefaligned.mdcrd
WaterNo
_idNAFlex_2lef_CG
datasetArray
date2024-Jul-05
descriptionDNA-B Duplex Naked
forceFieldCGeNArate
ionsModel-
moleculeTypeDna
rev_sequenceGAGCTTCAAAGGGTG
saltConcentration-
sequenceCACCCTTTGAAGCTC
soluteAtoms30
soluteCharge-
soluteResidues30
solventAtoms-
solventResidues-
time1,000
totalAtoms30
totalCharge-
totalIons-
totalResidues30
Quality Control
RMSd5.448 (0.664) Å    
Rgyr15.945 (0.357) Å    
SASA2667.139 (15.056) Ų    
RMSf