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_TF_3v79_9_dna_wholeA
Nucleic Acid Data:
Sequence
GTTACTGTXGGAAAGAAA
Rev. Sequence
TTTCTTTCCCACAGTAAC
Type
DNA
SubType
B
Chains
duplex
Pdb
-
Ligands
No
Keywords
DNA-B Duplex Naked TIP3P Electroneutral
MD Simulation >>
(Click to expand/shrink)
Simulation Metadata
Force Field
parmBSC1
Simulation Date
0.00000000 1656633600
Simulated Time
200
Time Step
2 ps
Parts
DNA
Temperature
300K
Water
TIP3P
Additional Solvent
No
Counter Ions
K+Cl-
Ionic Concentration
Electroneutrality
Additional Ions
150 mM
Additional Molecules
No
Ions Parameters
Dang
Unified Molecular Modeling (UMM) Metadata
(Click to see
full
UMM)
Simulation Metadata (UMM)
AdditionalIons
150 mM
AdditionalMolecules
No
AdditionalSolvent
No
Author
M.W.
Chains
duplex
Comments
Milosz MSCA
CounterIons
K+Cl-
Format
xtc
FrameStep
2 ps
Frames
250
IonicConcentration
Electroneutrality
IonsParameters
Dang
Ligands
No
NucType
DNA
PDB
-
Parts
DNA
RMSd_avg
3.049
RMSd_stdev
0.651
Rgyr_avg
18.688
Rgyr_stdev
0.513
SASA_avg
6475.956
SASA_stdev
153.122
SubType
B
Temperature
300K
Topology
whole.pdb
Trajectory
whole.xtc
Water
TIP3P
_id
NAFlex_TF_3v79_9_dna_wholeA
dataset
Array
date
0.00000000 1656633600
description
DNA-B Duplex Naked TIP3P Electroneutral
forceField
parmBSC1
ionsModel
-
moleculeType
Dna
rev_sequence
TTTCTTTCCCACAGTAAC
saltConcentration
-
sequence
GTTACTGTXGGAAAGAAA
soluteAtoms
1145
soluteCharge
-
soluteResidues
36
solventAtoms
-
solventResidues
-
time
200
totalAtoms
1145
totalCharge
-
totalIons
-
totalResidues
36
Quality Control
RMSd
-
Rgyr
-
SASA
-
RMSf
-
Trajectory Analyses >>
(Click to expand/shrink)