Entry: NAFlex_56merL_CG


Nucleic Acid Data:


SequenceCGCCGGCAGTAGCCGAAAAAATAGGCGCGCGCTCAAAAAAATGCCCCATGCCGCGC
Rev. SequenceGCGCGGCATGGGGCATTTTTTTGAGCGCGCGCCTATTTTTTCGGCTACTGCCGGCG
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_avg6.709
RMSd_stdev2.305
Rgyr_avg53.791
Rgyr_stdev1.083
SASA_avg9899.217
SASA_stdev48.174
SubTypeB
Temperature298K
Topology56merLStripped.pdb
Trajectory56merLaligned.pdb
WaterNo
_idNAFlex_56merL_CG
datasetArray
date2024-Jul-05
descriptionDNA-B Duplex Naked
forceFieldCGeNArate
ionsModel-
moleculeTypeDna
rev_sequenceGCGCGGCATGGGGCATTTTTTTGAGCGCGCGCCTATTTTTTCGGCTACTGCCGGCG
saltConcentration-
sequenceCGCCGGCAGTAGCCGAAAAAATAGGCGCGCGCTCAAAAAAATGCCCCATGCCGCGC
soluteAtoms112
soluteCharge-
soluteResidues112
solventAtoms-
solventResidues-
time1,000
totalAtoms112
totalCharge-
totalIons-
totalResidues112
Quality Control
RMSd6.709 (2.305) Å    
Rgyr53.791 (1.083) Å    
SASA9899.217 (48.174) Ų    
RMSf