Entry: NAFlex_AGCG


Nucleic Acid Data:


SequenceGCCGAGCGAGCGAGCGGC
Rev. SequenceGCCGCTCGCTCGCTCGGC
TypeDNA
SubTypeB
Chainsduplex
Pdb-
LigandsNo
KeywordsDNA-B Duplex Naked ParmBSC1 SPC/E AddedSalt


Simulation Metadata
Force FieldparmBSC1
Simulation Date2015-Apr-20
Simulated Time1,000 ns
Time Step1 ps
PartsDNA+ions
Temperature298K
WaterSPCE
Additional SolventNo
Counter IonsK+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
AuthorP.D.
Chainsduplex
CommentsmuABC / Last 250 ns (so 250000 frames out of 1M)
CounterIonsK+Cl-
Formatmdcrd
FrameStep1 ps
Frames1000000
IonicConcentration0.15M
IonsParametersDang
LigandsNo
NucTypeDNA
PDBNONE
PartsDNA+ions
RMSd_avg2.257
RMSd_stdev0.489
Rgyr_avg18.318
Rgyr_stdev0.349
SASA_avg6327.248
SASA_stdev95.667
SubTypeB
Temperature298K
TopologyAGCG_nowat.prmtop
TrajectoryAGCG_last250ns.trj
WaterSPCE
_idNAFlex_AGCG
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-20
descriptionDNA-B Duplex Naked ParmBSC1 SPC/E AddedSalt
forceFieldparmBSC1
ionsModel-
moleculeTypeDna
rev_sequenceGCCGCTCGCTCGCTCGGC
saltConcentration-
sequenceGCCGAGCGAGCGAGCGGC
soluteAtoms1135
soluteCharge-34
soluteResidues36
solventAtoms-
solventResidues-
time1,000
totalAtoms1135
totalCharge-34
totalIons-
totalResidues36
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-