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BigNASim
Entry: NAFlex_DTipDang015M_CG
Nucleic Acid Data:
Sequence
CGCGAATTCGCG
Rev. Sequence
CGCGAATTCGCG
Type
DNA
SubType
B
Chains
duplex
Pdb
-
Ligands
No
Keywords
DNA-B Duplex Naked
MD Simulation >>
(Click to expand/shrink)
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
1.640
RMSd_stdev
0.252
Rgyr_avg
13.431
Rgyr_stdev
0.259
SASA_avg
2124.390
SASA_stdev
12.985
SubType
B
Temperature
298K
Topology
DTipDang015MStripped.pdb
Trajectory
DTipDang015Maligned.mdcrd
Water
No
_id
NAFlex_DTipDang015M_CG
dataset
Array
date
0.00000000 1720396800
description
DNA-B Duplex Naked
forceField
CGeNArate
ionsModel
-
moleculeType
Dna
rev_sequence
CGCGAATTCGCG
saltConcentration
-
sequence
CGCGAATTCGCG
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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