Entry: NAFlex_lks2


Nucleic Acid Data:


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


Simulation Metadata
Force FieldparmBSC1
Simulation Date2014-Oct-01
Simulated Time1,000 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
Comments-
CounterIonsNa+
Formatnetcdf
FrameStep1ps
Frames1000000
IonicConcentrationElectroneutrality
IonsParametersDang
LigandsNo
NucTypeDNA
PDBNONE
PartsDNA+ions
RMSd_avg26.483
RMSd_stdev17.046
Rgyr_avg28.482
Rgyr_stdev15.619
SASA_avg5602.979
SASA_stdev379.012
SubTypeB
Temperature298K
Topologylks2_nowat.prmtop
Trajectorylks2_1-1000.nc
WaterTIP3P
_idNAFlex_lks2
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
date2014-Oct-01
descriptionDNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
forceFieldparmBSC1
ionsModel-
moleculeTypeDna
rev_sequenceAATGAGTCATCCACCTAG
saltConcentration-
sequenceCTAGGTGGATGACTCATT
soluteAtoms1142
soluteCharge-34
soluteResidues36
solventAtoms-
solventResidues-
time1,000
totalAtoms1142
totalCharge-34
totalIons-
totalResidues36
Quality Control
RMSd26.483 (17.046) Å    
Rgyr28.482 (15.619) Å    
SASA5602.979 (379.012) Ų    
RMSf