Entry: NAFlex_lks4


Nucleic Acid Data:


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


Simulation Metadata
Force FieldparmBSC1
Simulation Date2015-May-05
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_avg6.909
RMSd_stdev2.584
Rgyr_avg18.285
Rgyr_stdev0.473
SASA_avg6429.520
SASA_stdev155.304
SubTypeB
Temperature298K
Topologylks4_nowat.prmtop
Trajectorylks4_1-1000.nc
WaterTIP3P
_idNAFlex_lks4
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-May-05
descriptionDNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
forceFieldparmBSC1
ionsModel-
moleculeTypeDna
rev_sequenceCCGCGCGTGGTGCGCGCC
saltConcentration-
sequenceGGCGCGCACCACGCGCGG
soluteAtoms1134
soluteCharge-34
soluteResidues36
solventAtoms-
solventResidues-
time1,000
totalAtoms1134
totalCharge-34
totalIons-
totalResidues36
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-