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Entry: NAFlex_2l8q_CG
Nucleic Acid Data:
Sequence
CGCATGCTACGC
Rev. Sequence
GCGTAGCATGCG
Type
DNA
SubType
B
Chains
duplex
Pdb
-
Ligands
No
Keywords
DNA-B Duplex Naked
MD Simulation >>
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Simulation Metadata
Force Field
parmBSC1
Simulation Date
0.00000000 1720396800
Simulated Time
1,000
Time Step
20 ps
Parts
DNA
Temperature
298K
Water
No
Additional Solvent
No
Counter Ions
No
Ionic Concentration
No
Additional Ions
No
Additional Molecules
No
Ions Parameters
No
Unified Molecular Modeling (UMM) Metadata
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full
UMM)
Simulation Metadata (UMM)
AdditionalIons
No
AdditionalMolecules
No
AdditionalSolvent
No
Author
D.F.
Chains
duplex
Comments
CGeNArate: A Sequence-Dependent Coarse-Grained Model of DNA for Accurate Atomistic MD Simulations of kb-long Duplexes, DOI: 10.1093/nar/gkae444
CounterIons
No
Format
mdcrd
FrameStep
20 ps
Frames
50000
IonicConcentration
No
IonsParameters
No
Ligands
No
NucType
DNA
PDB
NONE
Parts
DNA
RMSd_avg
2.531
RMSd_stdev
0.386
Rgyr_avg
13.419
Rgyr_stdev
0.294
SASA_avg
2129.825
SASA_stdev
13.184
SubType
B
Temperature
298K
Topology
2l8qStripped.pdb
Trajectory
2l8qaligned.mdcrd
Water
No
_id
NAFlex_2l8q_CG
dataset
Array
date
0.00000000 1720396800
description
DNA-B Duplex Naked
forceField
CGeNArate
ionsModel
-
moleculeType
Dna
rev_sequence
GCGTAGCATGCG
saltConcentration
-
sequence
CGCATGCTACGC
soluteAtoms
24
soluteCharge
-
soluteResidues
24
solventAtoms
-
solventResidues
-
time
1,000
totalAtoms
24
totalCharge
-
totalIons
-
totalResidues
24
Quality Control
RMSd
-
Rgyr
-
SASA
-
RMSf
-
Trajectory Analyses >>
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