Entry: NAFlex_muAGAG


Nucleic Acid Data:


SequenceGCAGAGAGAGAGAGAGGC
Rev. SequenceGCCTCTCTCTCTCTCTGC
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_avg2.968
RMSd_stdev0.757
Rgyr_avg18.230
Rgyr_stdev0.425
SASA_avg6435.273
SASA_stdev97.802
SubTypeB
Temperature298K
TopologyTCGA_nowat.prmtop
TrajectoryTCGA_last250ns.trj
WaterSPCE
_idNAFlex_muAGAG
boxAngle109.471219
boxX80.6899552
boxY80.6899552
boxZ80.6899552
datasetArray
date2016-May-04
descriptionDNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt
forceFieldparmBSC0
ionsModel-
moleculeTypeDna
rev_sequenceGCCTCTCTCTCTCTCTGC
saltConcentration-
sequenceGCAGAGAGAGAGAGAGGC
soluteAtoms1139
soluteCharge-34
soluteResidues36
solventAtoms-
solventResidues-
time1,000
totalAtoms1139
totalCharge-34
totalIons-
totalResidues36
Quality Control
RMSd2.968 (0.757) Å    
Rgyr18.230 (0.425) Å    
SASA6435.273 (97.802) Ų    
RMSf