Entry: NAFlex_GGGT


Nucleic Acid Data:


SequenceGCGTGGGTGGGTGGGTGC
Rev. SequenceGCACCCACCCACCCACGC
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_avg4.236
RMSd_stdev0.813
Rgyr_avg18.481
Rgyr_stdev0.451
SASA_avg6372.597
SASA_stdev99.773
SubTypeB
Temperature300K
TopologyGGGT.dry.top
TrajectoryGGGT_250ions.trj.gz
WaterSPCE
_idNAFlex_GGGT
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_sequenceGCACCCACCCACCCACGC
saltConcentration-
sequenceGCGTGGGTGGGTGGGTGC
soluteAtoms1136
soluteCharge-34
soluteResidues36
solventAtoms-
solventResidues-
time1,000
totalAtoms1136
totalCharge-34
totalIons-
totalResidues36
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-