Entry: NAFlex_muGATA


Nucleic Acid Data:


SequenceGCTAGATAGATAGATAGC
Rev. SequenceGCTATCTATCTATCTAGC
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_avg3.329
RMSd_stdev0.762
Rgyr_avg18.061
Rgyr_stdev0.465
SASA_avg6511.414
SASA_stdev98.128
SubTypeB
Temperature298K
TopologyTCGA_nowat.prmtop
TrajectoryTCGA_last250ns.trj
WaterSPCE
_idNAFlex_muGATA
boxAngle109.471219
boxX80.7683931
boxY80.7683931
boxZ80.7683931
datasetArray
date2016-May-03
descriptionDNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt
forceFieldparmBSC0
ionsModel-
moleculeTypeDna
rev_sequenceGCTATCTATCTATCTAGC
saltConcentration-
sequenceGCTAGATAGATAGATAGC
soluteAtoms1143
soluteCharge-34
soluteResidues36
solventAtoms-
solventResidues-
time1,000
totalAtoms1143
totalCharge-34
totalIons-
totalResidues36
Quality Control
RMSd3.329 (0.762) Å    
Rgyr18.061 (0.465) Å    
SASA6511.414 (98.128) Ų    
RMSf