Entry: NAFlex_muGGGA


Nucleic Acid Data:


SequenceGCGAGGGAGGGAGGGAGC
Rev. SequenceGCTCCCTCCCTCCCTCGC
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_avg3.876
RMSd_stdev0.865
Rgyr_avg18.204
Rgyr_stdev0.488
SASA_avg6365.837
SASA_stdev112.369
SubTypeB
Temperature298K
TopologyTCGA_nowat.prmtop
TrajectoryTCGA_last250ns.trj
WaterSPCE
_idNAFlex_muGGGA
boxAngle109.471219
boxX80.6494386
boxY80.6494386
boxZ80.6494386
datasetArray
date2016-May-03
descriptionDNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt
forceFieldparmBSC0
ionsModel-
moleculeTypeDna
rev_sequenceGCTCCCTCCCTCCCTCGC
saltConcentration-
sequenceGCGAGGGAGGGAGGGAGC
soluteAtoms1136
soluteCharge-34
soluteResidues36
solventAtoms-
solventResidues-
time1,000
totalAtoms1136
totalCharge-34
totalIons-
totalResidues36
Quality Control
RMSd3.876 (0.865) Å    
Rgyr18.204 (0.488) Å    
SASA6365.837 (112.369) Ų    
RMSf