Entry: NAFlex_muCGCG


Nucleic Acid Data:


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


Simulation Metadata
Force FieldparmBSC1
Simulation Date2016-May-03
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_avg2.634
RMSd_stdev0.560
Rgyr_avg18.321
Rgyr_stdev0.401
SASA_avg6344.523
SASA_stdev103.496
SubTypeB
Temperature298K
TopologyTCGA_nowat.prmtop
TrajectoryTCGA_last250ns.trj
WaterSPCE
_idNAFlex_muCGCG
boxAngle109.471219
boxX80.6483481
boxY80.6483481
boxZ80.6483481
datasetArray
date2016-May-03
descriptionDNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt
forceFieldparmBSC0
ionsModel-
moleculeTypeDna
rev_sequenceGCCGCGCGCGCGCGCGGC
saltConcentration-
sequenceGCCGCGCGCGCGCGCGGC
soluteAtoms1132
soluteCharge-34
soluteResidues36
solventAtoms-
solventResidues-
time1,000
totalAtoms1132
totalCharge-34
totalIons-
totalResidues36
Quality Control
RMSd2.634 (0.560) Å    
Rgyr18.321 (0.401) Å    
SASA6344.523 (103.496) Ų    
RMSf