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_Naked_RNA_RNA
Nucleic Acid Data:
Sequence
CGCGAA
Rev. Sequence
UUCGCG
Type
RNA
SubType
A
Chains
duplex
Pdb
-
Ligands
No
Keywords
RNA-A Duplex Naked SPC/E AddedSalt
MD Simulation >>
(Click to expand/shrink)
Simulation Metadata
Force Field
parmBSC1
Simulation Date
0.00000000 1650585600
Simulated Time
250
Time Step
20 ps
Parts
DNA+ions
Temperature
298K
Water
SPCE
Additional Solvent
No
Counter Ions
Na+Cl-
Ionic Concentration
0.05M
Additional Ions
No
Additional Molecules
No
Ions Parameters
Dang
Unified Molecular Modeling (UMM) Metadata
(Click to see
full
UMM)
Simulation Metadata (UMM)
AdditionalIons
No
AdditionalMolecules
No
AdditionalSolvent
No
Author
V.G.
Chains
duplex
Comments
-
CounterIons
Na+Cl-
Format
xtc
FrameStep
20 ps
Frames
12500
IonicConcentration
0.05M
IonsParameters
Dang
Ligands
No
NucType
RNA
PDB
NONE
Parts
DNA+ions
RMSd_avg
3.368
RMSd_stdev
0.596
Rgyr_avg
12.832
Rgyr_stdev
0.516
SASA_avg
4503.290
SASA_stdev
85.688
SubType
A
Temperature
298K
Topology
structure.stripped.top
Trajectory
structure.stripped.xtc
Water
SPCE
_id
NAFlex_Naked_RNA_RNA
dataset
Array
date
0.00000000 1650585600
description
RNA-A Duplex Naked SPC/E AddedSalt
forceField
parmBSC1
ionsModel
-
moleculeType
Rna
rev_sequence
UUCGCG
saltConcentration
-
sequence
CGCGAA
soluteAtoms
770
soluteCharge
-
soluteResidues
24
solventAtoms
-
solventResidues
-
time
250
totalAtoms
770
totalCharge
-
totalIons
-
totalResidues
24
Quality Control
RMSd
-
Rgyr
-
SASA
-
RMSf
-
Trajectory Analyses >>
(Click to expand/shrink)