Entry: NAFlex_muAGCT


Nucleic Acid Data:


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


Simulation Metadata
Force FieldparmBSC1
Simulation Date2016-May-02
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_avg3.435
RMSd_stdev0.741
Rgyr_avg18.228
Rgyr_stdev0.416
SASA_avg6396.728
SASA_stdev101.170
SubTypeB
Temperature298K
TopologyTCGA_nowat.prmtop
TrajectoryTCGA_last250ns.trj
WaterSPCE
_idNAFlex_muAGCT
boxAngle109.471219
boxX80.7760765
boxY80.7760765
boxZ80.7760765
datasetArray
date2016-May-02
descriptionDNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt
forceFieldparmBSC0
ionsModel-
moleculeTypeDna
rev_sequenceGCAGCTAGCTAGCTAGGC
saltConcentration-
sequenceGCCTAGCTAGCTAGCTGC
soluteAtoms1139
soluteCharge-34
soluteResidues36
solventAtoms-
solventResidues-
time1,000
totalAtoms1139
totalCharge-34
totalIons-
totalResidues36
Quality Control
RMSd3.435 (0.741) Å    
Rgyr18.228 (0.416) Å    
SASA6396.728 (101.170) Ų    
RMSf