Entry: NAFlex_rna4


Nucleic Acid Data:


SequenceGGCGCGCACCACGCGCGG
Rev. SequenceCCGCGCGUGGUGCGCGCC
TypeRNA
SubTypeA
Chainsduplex
Pdb-
LigandsNo
KeywordsRNA-A Duplex Naked ParmBSC0 TIP3P Electroneutral


Simulation Metadata
Force FieldparmBSC1
Simulation Date2015-Apr-25
Simulated Time201 ns
Time Step10ps
Partsonly RNA
Temperature300K
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
AuthorI.F.
Chainsduplex
CommentsRNA4 from Faustino et al. (2010)
CounterIonsNa+
Formatmdcrd
FrameStep10ps
Frames20152
IonicConcentrationElectroneutrality
IonsParametersDang
LigandsNo
NucTypeRNA
PDBNONE
Partsonly RNA
RMSd_avg2.289
RMSd_stdev0.576
Rgyr_avg16.959
Rgyr_stdev0.649
SASA_avg6625.336
SASA_stdev100.348
SubTypeA
Temperature300K
Topologyrna4.vac.top
Trajectoryrna4.dry.trj.gz
WaterTIP3P
_idNAFlex_rna4
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
descriptionRNA-A Duplex Naked ParmBSC0 TIP3P Electroneutral
forceFieldparmBSC0
ionsModel-
moleculeTypeRna
rev_sequenceCCGCGCGUGGUGCGCGCC
saltConcentration-
sequenceGGCGCGCACCACGCGCGG
soluteAtoms1164
soluteCharge-34
soluteResidues36
solventAtoms-
solventResidues-
time201
totalAtoms1164
totalCharge-34
totalIons-
totalResidues36
Quality Control
RMSd2.289 (0.576) Å    
Rgyr16.959 (0.649) Å    
SASA6625.336 (100.348) Ų    
RMSf