Entry: NAFlex_muAGGC


Nucleic Acid Data:


SequenceGCGCAGGCAGGCAGGCGC
Rev. SequenceGCGCCTGCCTGCCTGCGC
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_avg2.819
RMSd_stdev0.612
Rgyr_avg18.154
Rgyr_stdev0.410
SASA_avg6380.351
SASA_stdev97.913
SubTypeB
Temperature298K
TopologyTCGA_nowat.prmtop
TrajectoryTCGA_last250ns.trj
WaterSPCE
_idNAFlex_muAGGC
boxAngle109.471219
boxX80.7761607
boxY80.7761607
boxZ80.7761607
datasetArray
date2016-May-02
descriptionDNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt
forceFieldparmBSC0
ionsModel-
moleculeTypeDna
rev_sequenceGCGCCTGCCTGCCTGCGC
saltConcentration-
sequenceGCGCAGGCAGGCAGGCGC
soluteAtoms1135
soluteCharge-34
soluteResidues36
solventAtoms-
solventResidues-
time1,000
totalAtoms1135
totalCharge-34
totalIons-
totalResidues36
Quality Control
RMSd2.819 (0.612) Å    
Rgyr18.154 (0.410) Å    
SASA6380.351 (97.913) Ų    
RMSf