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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 >>
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Simulation Metadata
Force Field
parmBSC1
Simulation Date
2022-Jul-01
Simulated Time
200 ns
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
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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
2022-Jul-01
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
3.049 (0.651) Å
Rgyr
18.688 (0.513) Å
SASA
6475.956 (153.122) Ų
RMSf
Trajectory Analyses >>
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