|
Id. |
PDB |
Type |
SubType |
ForceField |
Solvent |
Description |
Time (ns) |
Sequence |
|
NAFlex_D05M |
1BNA |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
3,000 |
CGCGAATTCGCG |
|
NAFlex_DTipDang015M |
1BNA |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
2,000 |
CGCGAATTCGCG |
|
NAFlex_BSC1-BSC0 |
1NAJ |
Dna |
B |
parmBSC0 |
TIP3P |
DNA-B Duplex Naked TIP3P Electroneutral ParmBSC0 |
1,500 |
CGCGAATTCGCG |
|
NAFlex_BSC1-C36 |
1NAJ |
Dna |
B |
Charmm36 |
TIP3P |
DNA-B Duplex Naked Charmm36 TIP3P Electroneutral |
1,500 |
CGCGAATTCGCGCGCGAATTCGCG |
|
NAFlex_BSC1-Garcia |
1NAJ |
Dna |
B |
ParmBSC0-CG |
TIP3P |
DNA-B Duplex Naked Cheng-Garcia TIP3P Electroneutral |
1,500 |
CGCGAATTCGCG |
|
NAFlex_BSC1-OL1 |
1NAJ |
Dna |
B |
ParmBSC0-OL1 |
TIP3P |
DNA-B Duplex Naked OL1 TIP3P Electroneutral |
1,500 |
CGCGAATTCGCG |
|
NAFlex_BSC1-OL1-OL4 |
1NAJ |
Dna |
B |
ParmBSC0-OL1-OL4 |
TIP3P |
DNA-B Duplex Naked OL1+OL4 TIP3P Electroneutral |
1,500 |
CGCGAATTCGCG |
|
NAFlex_BSC1-OL4 |
1NAJ |
Dna |
B |
ParmBSC0-OL4 |
TIP3P |
DNA-B Duplex Naked OL4 TIP3P Electroneutral |
1,500 |
CGCGAATTCGCG |
|
NAFlex_DDD_II |
1BNA |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked DDD ParmBSC1 TIP3P Electroneutral |
1,200 |
CGCGAATTCGCG |
|
NAFlex_2mhi |
2MHI |
Rna |
A |
parmBSC0 |
TIP3P |
RNA-A Duplex Naked ParmBSC0 TIP3P Electroneutral Telomerase |
1,027 |
GGAAACGCCGCGGUCAGCUCGGCUGCUGCGAAGAGUUCGUCUCUGUUGUUUCC |
|
NAFlex_GAGA_RNA |
1Q9A |
Rna |
A |
parmBSC0 |
TIP3P |
RNA-A Single Stranded Naked ParmBSC0 TIP3P Electroneutral Sarcin-Ricin Hairpin loop Flipout-bases |
1,022 |
CGCGAGAGCG |
|
NAFlex_1pqt |
1PQT |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Single Stranded Naked ParmBSC1 TIP3P AddedSalt Hairpin |
1,000 |
GCGAAGC |
|
NAFlex_AGCG |
NONE |
Dna |
B |
parmBSC1 |
SPCE |
DNA-B Duplex Naked ParmBSC1 SPC/E AddedSalt |
1,000 |
GCCGAGCGAGCGAGCGGC |
|
NAFlex_GGGA |
NONE |
Dna |
B |
parmBSC1 |
SPCE |
DNA-B Duplex Naked ParmBSC1 SPC/E AddedSalt |
1,000 |
GCGAGGGAGGGAGGGAGC |
|
NAFlex_DDD_II_1 |
1NAJ |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked DDD ParmBSC1 TIP3P Electroneutral |
1,000 |
CGCGAATTCGCG |
|
NAFlex_DDD_II_2 |
1NAJ |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked DDD ParmBSC1 TIP3P Electroneutral |
1,000 |
CGCGAATTCGCG |
|
NAFlex_DSpcCheatham |
1BNA |
Dna |
B |
parmBSC1 |
SPCE |
DNA-B Duplex Naked ParmBSC1 SPC/E Electroneutral |
1,000 |
CGCGAATTCGCG |
|
NAFlex_DSpcDang |
1BNA |
Dna |
B |
parmBSC1 |
SPCE |
DNA-B Duplex Naked ParmBSC1 SPC/E Electroneutral |
1,000 |
CGCGAATTCGCG |
|
NAFlex_DTipCheatham |
1BNA |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral |
1,000 |
CGCGAATTCGCG |
|
NAFlex_muAGGA |
NONE |
Dna |
B |
parmBSC0 |
SPCE |
DNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt |
1,000 |
GCGAAGGAAGGAAGGAGC |
|
NAFlex_muCGGA |
NONE |
Dna |
B |
parmBSC0 |
SPCE |
DNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt |
1,000 |
GCGACGGACGGACGGAGC |
|
NAFlex_muGGGA |
NONE |
Dna |
B |
parmBSC0 |
SPCE |
DNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt |
1,000 |
GCGAGGGAGGGAGGGAGC |
|
NAFlex_muTCGA |
NONE |
Dna |
B |
parmBSC1 |
SPCE |
DNA-B Duplex Naked ParmBSC1 SPC/E AddedSalt |
1,000 |
GCGATCGATCGATCGAGC |
|
NAFlex_muTGGA |
NONE |
Dna |
B |
parmBSC0 |
SPCE |
DNA-B Duplex Naked ParmBSC0 SPC/E AddedSalt |
1,000 |
GCGATGGATGGATGGAGC |
|
NAFlex_miniABC_NaK_7 |
NONE |
Dna |
B |
parmBSC1 |
SPC/E |
B-DNA Duplex Naked ParmBSC1 SPC/E 0.15 mol NaCl/KCl 50%/50% |
1,000 |
GCGACCGAATGTAATTGC |
|
NAFlex_miniABC_K_12 |
NONE |
Dna |
B |
parmBSC1 |
SPC/E |
B-DNA Duplex Naked ParmBSC1 SPC/E 0.15 mol KCl |
1,000 |
GCTGGCATGAAGCGACGC |
|
NAFlex_miniABC_K_6 |
NONE |
Dna |
B |
parmBSC1 |
SPC/E |
B-DNA Duplex Naked ParmBSC1 SPC/E 0.15 mol KCl |
1,000 |
GCGAACTCAAAGGTTGGC |
|
NAFlex_miniABC_K_7 |
NONE |
Dna |
B |
parmBSC1 |
SPC/E |
B-DNA Duplex Naked ParmBSC1 SPC/E 0.15 mol KCl |
1,000 |
GCGACCGAATGTAATTGC |
|
NAFlex_miniABC_Na_12 |
NONE |
Dna |
B |
parmBSC1 |
SPC/E |
B-DNA Duplex Naked ParmBSC1 SPC/E 0.15 mol NaCl |
1,000 |
GCTGGCATGAAGCGACGC |
|
NAFlex_miniABC_Na_6 |
NONE |
Dna |
B |
parmBSC1 |
SPC/E |
B-DNA Duplex Naked ParmBSC1 SPC/E 0.15 mol NaCl |
1,000 |
GCGAACTCAAAGGTTGGC |
|
NAFlex_miniABC_Na_7 |
NONE |
Dna |
B |
parmBSC1 |
SPC/E |
B-DNA Duplex Naked ParmBSC1 SPC/E 0.15 mol NaCl |
1,000 |
GCGACCGAATGTAATTGC |
|
NAFlex_miniABC_NaK_12 |
NONE |
Dna |
B |
parmBSC1 |
SPC/E |
B-DNA Duplex Naked ParmBSC1 SPC/E 0.15 mol NaCl/KCl 50%/50% |
1,000 |
GCTGGCATGAAGCGACGC |
|
NAFlex_miniABC_NaK_6 |
NONE |
Dna |
B |
parmBSC1 |
SPC/E |
B-DNA Duplex Naked ParmBSC1 SPC/E 0.15 mol NaCl/KCl 50%/50% |
1,000 |
GCGAACTCAAAGGTTGGC |
|
NAFlex_RNA_miniABC_KCl_6 |
NONE |
Rna |
A |
parmBSC0+OL3 |
TIP3P |
RNA-A Duplex Naked TIP3P AddedSalt |
1,000 |
GCGAACUCAAAGGUUGGC |
|
NAFlex_RNA_miniABC_KCl_7 |
NONE |
Rna |
A |
parmBSC0+OL3 |
TIP3P |
RNA-A Duplex Naked TIP3P AddedSalt |
1,000 |
GCGACCGAAUGUAAUUGC |
|
NAFlex_RNA_miniABC_KCl_12 |
NONE |
Rna |
A |
parmBSC0+OL3 |
TIP3P |
RNA-A Duplex Naked TIP3P AddedSalt |
1,000 |
GCUGGCAUGAAGCGACGC |
|
NAFlex_DDD_800ns |
1NAJ |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked DDD ParmBSC1 TIP3P Electroneutral |
800 |
CGCGAATTCGCG |
|
NAFlex_56merTIP3P |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral |
500 |
CGCGATTGCCTAACGGACAGGCATAGACGTCTATGCCTGTCCGTTAGGCAATCGCG |
|
NAFlex_ACGT |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral |
500 |
CGCGACGTCGCG |
|
NAFlex_CTAG_12 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGTCTACTAGCGAGGC |
|
NAFlex_CTAG_16 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGTCTCCTAGCGAGGC |
|
NAFlex_CTAG_19 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P AddedSalt |
500 |
CGTCTGCTAGCGAGGC |
|
NAFlex_colibactin1 |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked TIP3P Electroneutral |
400 |
CGCGAAAATTTTCGCG |
|
NAFlex_36merSPCE |
NONE |
Dna |
B |
parmBSC1 |
SPCE |
DNA-B Duplex Naked ParmBSC1 SPC/E Electroneutral |
300 |
CGCGATTGCCTAACGAGTACTCGTTAGGCAATCGCG |
|
NAFlex_36merTIP3P |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral |
300 |
CGCGATTGCCTAACGAGTACTCGTTAGGCAATCGCG |
|
NAFlex_56merSPCE |
NONE |
Dna |
B |
parmBSC1 |
SPCE |
DNA-B Duplex Naked ParmBSC1 SPC/E Electroneutral |
290 |
CGCGATTGCCTAACGGACAGGCATAGACGTCTATGCCTGTCCGTTAGGCAATCGCG |
|
NAFlex_ACGThmet |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked Parm99 TIP3P AddedSalt |
250 |
CGCGAXGTCGCG |
|
NAFlex_ACGTmet |
NONE |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked Parm99 TIP3P AddedSalt |
250 |
CGCGAXGTCGCG |
|
NAFlex_Naked_RNA_RNA |
NONE |
Rna |
A |
parmBSC1 |
SPCE |
RNA-A Duplex Naked SPC/E AddedSalt |
250 |
CGCGAA |
|
NAFlex_Naked_DNA_DNA |
NONE |
Dna |
B |
parmBSC1 |
SPCE |
DNA-B Duplex Naked SPC/E AddedSalt |
250 |
CGCGAA |
|
NAFlex_Naked_DNA_RNA |
NONE |
Rna |
B |
parmBSC1 |
SPCE |
-B Duplex Naked SPC/E AddedSalt |
250 |
CGCGAA |
|
NAFlex_A-Ethanol |
1BNA |
Dna |
A (in ethanol) |
parmBSC1 |
Wat-Ethanol |
DNA-A Duplex Naked ParmBSC1 Water-Ethanol Electroneutral |
200 |
CGCGAATTCGCG |
|
NAFlex_1d89 |
1D89 |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral |
200 |
CGCGAAAAAACG |
|
NAFlex_DDD_GMX_CPU |
1NAJ |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked DDD ParmBSC1 TIP3P Electroneutral |
100 |
CGCGAATTCGCG |
|
NAFlex_DDD_GMX_GPU |
1NAJ |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked DDD ParmBSC1 TIP3P Electroneutral |
100 |
CGCGAATTCGCG |
|
NAFlex_DDD_Amber_CPU |
1NAJ |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked DDD ParmBSC1 TIP3P Electroneutral |
100 |
CGCGAATTCGCG |
|
NAFlex_DDD_Amber_GPU |
1NAJ |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-B Duplex Naked DDD ParmBSC1 TIP3P Electroneutral |
100 |
CGCGAATTCGCG |
|
NAFlex_A2B_1 |
1BNA |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-Mixed Duplex Naked ParmBSC1 TIP3P Electroneutral Transition |
40 |
CGCGAATTCGCG |
|
NAFlex_A2B_2 |
1BNA |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-Mixed Duplex Naked ParmBSC1 TIP3P Electroneutral Transition |
40 |
CGCGAATTCGCG |
|
NAFlex_A2B_3 |
1BNA |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-Mixed Duplex Naked ParmBSC1 TIP3P Electroneutral Transition |
40 |
CGCGAATTCGCG |
|
NAFlex_A2B_4 |
1BNA |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-Mixed Duplex Naked ParmBSC1 TIP3P Electroneutral Transition |
40 |
CGCGAATTCGCG |
|
NAFlex_A2B_5 |
1BNA |
Dna |
B |
parmBSC1 |
TIP3P |
DNA-Mixed Duplex Naked ParmBSC1 TIP3P Electroneutral Transition |
40 |
CGCGAATTCGCG |
