Entry: NAFlex_ACGT


Nucleic Acid Data:


SequenceCGCGACGTCGCG
Rev. SequenceCGCGACGTCGCG
TypeDNA
SubTypeB
Chainsduplex
Pdb-
LigandsNo
KeywordsDNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral


Simulation Metadata
Force FieldparmBSC1
Simulation Date2015-Apr-25
Simulated Time500 ns
Time Step1ps
PartsDNA+ions
Temperature298K
WaterTIP3P
Additional SolventNo
Counter IonsNa+
Ionic ConcentrationElectroneutrality
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
Commentsonly last 250 ns (so 250000 frames out of 500000)
CounterIonsNa+
Formatmdcrd
FrameStep1ps
Frames500000
IonicConcentrationElectroneutrality
IonsParametersDang
LigandsNo
NucTypeDNA
PDBNONE
PartsDNA+ions
RMSd_avg1.704
RMSd_stdev0.298
Rgyr_avg13.192
Rgyr_stdev0.257
SASA_avg4337.973
SASA_stdev68.196
SubTypeB
Temperature298K
TopologyACGT_nowat.prmtp
TrajectoryACGT_last250ns_nowatReimg.crd
WaterTIP3P
_idNAFlex_ACGT
authorsIvan Ivani, Pablo D. Dans, Agnès Noy, Alberto Pérez, Ignacio Faustino, Adam Hospital, Jürgen Walther, Pau Andrio, Ramon Goñi, Alexandra Balaceanu, Guillem Portella, Federica Battistini, Josep Lluís Gelpí, Carlos González, Michele Vendruscolo, Charles A. Laughton, Sarah A. Harris, David A. Case and Modesto Orozco
datasetArray
date2015-Apr-25
descriptionDNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
forceFieldparmBSC1
ionsModel-
moleculeTypeDna
rev_sequenceCGCGACGTCGCG
saltConcentration-
sequenceCGCGACGTCGCG
soluteAtoms756
soluteCharge-22
soluteResidues24
solventAtoms-
solventResidues-
time500
totalAtoms756
totalCharge-22
totalIons-
totalResidues24
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-