Entry: NAFlex_ACGThmet


Nucleic Acid Data:


SequenceCGCGAXGTCGCG
Rev. SequenceCGCGAXGTCGCG
TypeDNA
SubTypeB
Chainsduplex
Pdb-
Ligands5-hydroxymethyl-cytosine
KeywordsDNA-B Duplex Naked Parm99 TIP3P AddedSalt


Simulation Metadata
Force FieldparmBSC1
Simulation Date2015-Apr-28
Simulated Time250 ns
Time Step1ps
PartsDNA
Temperature298K
WaterTIP3P
Additional SolventNo
Counter IonsNa+Cl-
Ionic Concentration0.15M
Additional IonsNo
Additional MoleculesNo
Ions ParametersDang
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
Simulation Metadata (UMM)
AdditionalIonsNo
AdditionalMoleculesNo
AdditionalSolventNo
AuthorA.H.
Chainsduplex
Comments-
CounterIonsNa+Cl-
Formatnetcdf
FrameStep1ps
Frames250000
IonicConcentration0.15M
IonsParametersDang
Ligands5-hydroxymethyl-cytosine
NucTypeDNA
PDBNONE
PartsDNA
RMSd_avg1.999
RMSd_stdev0.386
Rgyr_avg13.203
Rgyr_stdev0.267
SASA_avg1926.224
SASA_stdev172.132
SubTypeB
Temperature298K
TopologyACGThmet_ABC.dry.top
TrajectoryACGThmet_ABC.FULL.dry.netcdf
WaterTIP3P
_idNAFlex_ACGThmet
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-28
descriptionDNA-B Duplex Naked Parm99 TIP3P AddedSalt
forceFieldparmBSC1
ionsModel-
moleculeTypeDna
rev_sequenceCGCGAXGTCGCG
saltConcentration-
sequenceCGCGAXGTCGCG
soluteAtoms764
soluteCharge764
soluteResidues24
solventAtoms-
solventResidues-
time250
totalAtoms764
totalCharge764
totalIons-
totalResidues24
Quality Control
RMSd1.999 (0.386) Å    
Rgyr13.203 (0.267) Å    
SASA1926.224 (172.132) Ų    
RMSf