Entry: NAFlex_muGGGC


Nucleic Acid Data:


SequenceGCGCGGGCGGGCGGGCGC
Rev. SequenceGCGCCCGCCCGCCCGCGC
TypeDNA
SubTypeB
Chainsduplex
Pdb-
LigandsNo
KeywordsDNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt


Simulation Metadata
Force FieldparmBSC1
Simulation Date2016-May-04
Simulated Time1,000 ns
Time Step1 ps
PartsDNA+ions
Temperature298K
WaterSPCE
Additional SolventNo
Counter IonsK+Cl-
Ionic Concentration0.15M
Additional IonsNo
Additional MoleculesNo
Ions ParametersDang
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
Simulation Metadata (UMM)
AdditionalIonsNo
AdditionalMoleculesNo
AdditionalSolventNo
AuthorP.D.
Chainsduplex
CommentsmuABC
CounterIonsK+Cl-
Formatmdcrd
FrameStep1 ps
Frames1000000
IonicConcentration0.15M
IonsParametersDang
LigandsNo
NucTypeDNA
PDBNONE
PartsDNA+ions
RMSd_avg3.246
RMSd_stdev0.678
Rgyr_avg18.235
Rgyr_stdev0.431
SASA_avg6342.894
SASA_stdev112.667
SubTypeB
Temperature298K
TopologyTCGA_nowat.prmtop
TrajectoryTCGA_last250ns.trj
WaterSPCE
_idNAFlex_muGGGC
boxAngle109.471219
boxX80.7287913
boxY80.7287913
boxZ80.7287913
datasetArray
date2016-May-04
descriptionDNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt
forceFieldparmBSC0
ionsModel-
moleculeTypeDna
rev_sequenceGCGCCCGCCCGCCCGCGC
saltConcentration-
sequenceGCGCGGGCGGGCGGGCGC
soluteAtoms1132
soluteCharge-34
soluteResidues36
solventAtoms-
solventResidues-
time1,000
totalAtoms1132
totalCharge-34
totalIons-
totalResidues36
Quality Control
RMSd3.246 (0.678) Å    
Rgyr18.235 (0.431) Å    
SASA6342.894 (112.667) Ų    
RMSf