Entry: NAFlex_muATGC


Nucleic Acid Data:


SequenceGCGCATGCATGCATGCGC
Rev. SequenceGCGCATGCATGCATGCGC
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_avg4.074
RMSd_stdev0.804
Rgyr_avg18.109
Rgyr_stdev0.479
SASA_avg6459.843
SASA_stdev115.782
SubTypeB
Temperature298K
TopologyTCGA_nowat.prmtop
TrajectoryTCGA_last250ns.trj
WaterSPCE
_idNAFlex_muATGC
boxAngle109.471219
boxX80.6690892
boxY80.6690892
boxZ80.6690892
datasetArray
date2016-May-02
descriptionDNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt
forceFieldparmBSC0
ionsModel-
moleculeTypeDna
rev_sequenceGCGCATGCATGCATGCGC
saltConcentration-
sequenceGCGCATGCATGCATGCGC
soluteAtoms1138
soluteCharge-34
soluteResidues36
solventAtoms-
solventResidues-
time1,000
totalAtoms1138
totalCharge-34
totalIons-
totalResidues36
Quality Control
RMSd4.074 (0.804) Å    
Rgyr18.109 (0.479) Å    
SASA6459.843 (115.782) Ų    
RMSf