Home
News & Events
MuG project
Community
Compute Platform
MuG VRE Compute Platform
Data Manager
Application Offer
Help
Data
BigNASim
Tools
3C Tools Comparison
Flexibility Browser
TADkit 3D genome visualizer
Information Network
Bibliography
Molecular Modeling and Bioinformatics Group
Browse
Home
»
BigNASim
Entry: NAFlex_miniABC_13_CG
Nucleic Acid Data:
Sequence
GCTTGTGACGGCTAGGGC
Rev. Sequence
GCCCTAGCCGTCACAAGC
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 1719878400
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
(Click to see
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
2.617
RMSd_stdev
0.537
Rgyr_avg
18.821
Rgyr_stdev
0.389
SASA_avg
3196.501
SASA_stdev
17.794
SubType
B
Temperature
298K
Topology
Simulated13.pdb
Trajectory
Simulated13aligned.mdcrd
Water
No
_id
NAFlex_miniABC_13_CG
dataset
Array
date
0.00000000 1719878400
description
DNA-B Duplex Naked
forceField
CGeNArate
ionsModel
-
moleculeType
Dna
rev_sequence
GCCCTAGCCGTCACAAGC
saltConcentration
-
sequence
GCTTGTGACGGCTAGGGC
soluteAtoms
36
soluteCharge
-
soluteResidues
36
solventAtoms
-
solventResidues
-
time
1,000
totalAtoms
36
totalCharge
-
totalIons
-
totalResidues
36
Quality Control
RMSd
-
Rgyr
-
SASA
-
RMSf
-
Trajectory Analyses >>
(Click to expand/shrink)