Entry: NAFlex_GGGG


Nucleic Acid Data:


SequenceGCGGGGGGGGGGGGGGGC
Rev. SequenceGCCCCCCCCCCCCCCCGC
TypeDNA
SubTypeB
Chainsduplex
Pdb-
Ligandsno
KeywordsDNA-B Duplex Naked ParmBSC1 SPC/E AddedSalt


Simulation Metadata
Force FieldparmBSC1
Simulation Date2015-Apr-25
Simulated Time1,000 ns
Time Step1ps
Partsions + DNA
Temperature300K
WaterSPCE
Additional SolventNo
Counter IonsK+Cl-
Ionic Concentration0.15M
Additional IonsNo
Additional MoleculesNo
Ions Parameters-
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
Simulation Metadata (UMM)
AdditionalIonsNo
AdditionalMoleculesNo
AdditionalSolventNo
AuthorA.P.
Chainsduplex
Commentslast 250ns of simulation
CounterIonsK+Cl-
Formatmdcrd
FrameStep1ps
Frames1000000
IonicConcentration0.15M
IonsParameters-
Ligandsno
NucTypeDNA
PDBNONE
Partsions + DNA
RMSd_avg3.962
RMSd_stdev0.729
Rgyr_avg18.486
Rgyr_stdev0.484
SASA_avg6312.668
SASA_stdev95.603
SubTypeB
Temperature300K
TopologyGGGG.dry.top
TrajectoryGGGG_250ions.trj.gz
WaterSPCE
_idNAFlex_GGGG
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 ParmBSC1 SPC/E AddedSalt
forceFieldparmBSC1
ionsModel-
moleculeTypeDna
rev_sequenceGCCCCCCCCCCCCCCCGC
saltConcentration-
sequenceGCGGGGGGGGGGGGGGGC
soluteAtoms1132
soluteCharge-34
soluteResidues36
solventAtoms-
solventResidues-
time1,000
totalAtoms1132
totalCharge-34
totalIons-
totalResidues36
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-