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Entry: NAFlex_Naked_RpSp
Nucleic Acid Data:
Sequence
CXXXXX
Rev. Sequence
XXXXXX
Type
DNA+RNA
SubType
A
Chains
duplex
Pdb
-
Ligands
No
Keywords
-A Duplex Naked SPC/E AddedSalt
MD Simulation >>
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Simulation Metadata
Force Field
parmBSC1
Simulation Date
2022-Apr-28
Simulated Time
250 ns
Time Step
20 ps
Parts
DNA+RNA+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
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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
DNA+RNA
PDB
NONE
Parts
DNA+RNA+ions
RMSd_avg
3.151
RMSd_stdev
0.600
Rgyr_avg
13.447
Rgyr_stdev
0.386
SASA_avg
4448.444
SASA_stdev
75.261
SubType
A
Temperature
298K
Topology
structure.stripped.top
Trajectory
structure.stripped.xtc
Water
SPCE
_id
NAFlex_Naked_RpSp
dataset
Array
date
2022-Apr-28
description
-A Duplex Naked SPC/E AddedSalt
forceField
parmBSC1
ionsModel
-
moleculeType
Rna
rev_sequence
XXXXXX
saltConcentration
-
sequence
CXXXXX
soluteAtoms
764
soluteCharge
-
soluteResidues
24
solventAtoms
-
solventResidues
-
time
250
totalAtoms
764
totalCharge
-
totalIons
-
totalResidues
24
Quality Control
RMSd
3.151 (0.600) Å
Rgyr
13.447 (0.386) Å
SASA
4448.444 (75.261) Ų
RMSf
Trajectory Analyses >>
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