Entry: NAFlex_GGf


Nucleic Acid Data:


SequenceCCATACGATACGG
Rev. SequenceCCGTATGGTATGG
TypeDNA
SubTypeB
Chainsduplex
Pdb-
LigandsNo
KeywordsDNA-B Duplex Naked ModifiedNucleotides 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
Comments-
CounterIonsNa+
Formatmdcrd
FrameStep1ps
Frames500000
IonicConcentrationElectroneutrality
IonsParametersDang
LigandsNo
NucTypeDNA
PDBNONE
PartsDNA+ions
RMSd_avg2.246
RMSd_stdev0.476
Rgyr_avg14.246
Rgyr_stdev0.461
SASA_avg4782.951
SASA_stdev78.067
SubTypeB
Temperature298K
TopologyGGf_nowat.prmtop
TrajectoryGGf_last250ns_nowatReimg.mdcrd
WaterTIP3P
_idNAFlex_GGf
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 ModifiedNucleotides ParmBSC1 TIP3P Electroneutral
forceFieldparmBSC1
ionsModel-
moleculeTypeDna
rev_sequenceCCGTATGGTATGG
saltConcentration-
sequenceCCATACGATACGG
soluteAtoms826
soluteCharge-24
soluteResidues26
solventAtoms-
solventResidues-
time500
totalAtoms826
totalCharge-24
totalIons-
totalResidues26
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-