Entry: NAFlex_miniABC_2_CG


Nucleic Acid Data:


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


Simulation Metadata
Force FieldCGeNArate
Simulation Date2024-Jul-02
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_avg2.376
RMSd_stdev0.609
Rgyr_avg18.555
Rgyr_stdev0.447
SASA_avg3194.883
SASA_stdev17.876
SubTypeB
Temperature298K
TopologySimulated2.pdb
TrajectorySimulated2aligned.mdcrd
WaterNo
_idNAFlex_miniABC_2_CG
datasetArray
date2024-Jul-02
descriptionDNA-B Duplex Naked
forceFieldCGeNArate
ionsModel-
moleculeTypeDna
rev_sequenceGCTCCTGGTACTTATTGC
saltConcentration-
sequenceGCAATAAGTACCAGGAGC
soluteAtoms36
soluteCharge-
soluteResidues36
solventAtoms-
solventResidues-
time1,000
totalAtoms36
totalCharge-
totalIons-
totalResidues36
Quality Control
RMSd2.376 (0.609) Å    
Rgyr18.555 (0.447) Å    
SASA3194.883 (17.876) Ų    
RMSf