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Molecular Modeling and Bioinformatics Group

Entry: NAFlex_AT-rich_crowd_Arg_500mM


Nucleic Acid Data:


SequenceTGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGT
Rev. SequenceACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACA
TypeDNA
SubTypeB
ChainsMultiple duplex
Pdb-
LigandsNo
KeywordsDNA-B Duplex Naked TIP3P AddedSalt


Simulation Metadata
Force FieldparmBSC1
Simulation Date0.00000000 1638316800
Simulated Time5,000
Time Step20 ps
PartsDNA+ions
Temperature298K
WaterTIP3P
Additional SolventNo
Counter IonsNa+Cl-
Ionic Concentration0.5M
Additional IonsArg
Additional MoleculesNo
Ions ParametersJoung&Cheatham
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
Simulation Metadata (UMM)
AdditionalIonsArg
AdditionalMoleculesNo
AdditionalSolventNo
AuthorF.B.
ChainsMultiple duplex
CommentsLysArg project
CounterIonsNa+Cl-
Formatmdcrd
FrameStep20 ps
Frames250000
IonicConcentration0.5M
IonsParametersJoung&Cheatham
LigandsNo
NucTypeDNA
PDBNONE
PartsDNA+ions
RMSd_avg108.848
RMSd_stdev9.641
Rgyr_avg84.826
Rgyr_stdev7.697
SASA_avg38486.985
SASA_stdev2470.306
SubTypeB
Temperature298K
Topologymdp_first_frame_nowat_tleap.top
Trajectorytraj_nowat.trj
WaterTIP3P
_idNAFlex_AT-rich_crowd_Arg_500mM
datasetArray
date0.00000000 1638316800
descriptionDNA-B Duplex Naked TIP3P AddedSalt
forceFieldparmBSC1
ionsModel-
moleculeTypeDna
rev_sequenceACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACA
saltConcentration-
sequenceTGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGTACAAAATATACATGTATATTTTGT
soluteAtoms11460
soluteCharge11460
soluteResidues360
solventAtoms-
solventResidues-
time5,000
totalAtoms11460
totalCharge11460
totalIons-
totalResidues360
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-