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BigNASim
Entry: NAFlex_AT-rich_Na_25mM
Nucleic Acid Data:
Sequence
TATGTATATT
Rev. Sequence
TTGTAATTAA
Type
DNA
SubType
B
Chains
duplex
Pdb
-
Ligands
No
Keywords
DNA-B Duplex Naked SPC/E AddedSalt
MD Simulation >>
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Simulation Metadata
Force Field
parmBSC1
Simulation Date
0.00000000 1637712000
Simulated Time
400
Time Step
1 ps
Parts
DNA+ions
Temperature
298K
Water
SPCE
Additional Solvent
No
Counter Ions
K+Cl-
Ionic Concentration
0.025M
Additional Ions
Na
Additional Molecules
No
Ions Parameters
Dang
Unified Molecular Modeling (UMM) Metadata
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full
UMM)
Simulation Metadata (UMM)
AdditionalIons
Na
AdditionalMolecules
No
AdditionalSolvent
No
Author
F.B.
Chains
duplex
Comments
LysArg project
CounterIons
K+Cl-
Format
mdcrd
FrameStep
1 ps
Frames
400000
IonicConcentration
0.025M
IonsParameters
Dang
Ligands
No
NucType
DNA
PDB
NONE
Parts
DNA+ions
RMSd_avg
2.860
RMSd_stdev
0.721
Rgyr_avg
20.126
Rgyr_stdev
0.495
SASA_avg
7233.095
SASA_stdev
153.558
SubType
B
Temperature
298K
Topology
mdp_first_frame_nowat_tleap.top
Trajectory
traj_nowat.trj
Water
SPCE
_id
NAFlex_AT-rich_Na_25mM
dataset
Array
date
0.00000000 1637712000
description
DNA-B Duplex Naked SPC/E AddedSalt
forceField
parmBSC1
ionsModel
-
moleculeType
Dna
rev_sequence
TTGTAATTAA
saltConcentration
-
sequence
TATGTATATT
soluteAtoms
1276
soluteCharge
-38
soluteResidues
40
solventAtoms
-
solventResidues
-
time
400
totalAtoms
1276
totalCharge
-38
totalIons
-
totalResidues
40
Quality Control
RMSd
-
Rgyr
-
SASA
-
RMSf
-
Trajectory Analyses >>
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