Published June 2025
| Version v1
Dataset
Open
DNA minicircle (339 base pairs) with 31 turns 30ns
Description
DNA minicircle (339 base pairs) with 31 turns 30ns, 100mM CaCl2.
Trajectory originally donated to SlimMD
Files
snapshot.png
Files
(26.4 MB)
| Name | Size | Download all |
|---|---|---|
|
md5:e31e724d19591828cc42dc16d275facb
|
970.5 kB | Download |
|
md5:8a051511ac3e54233f8e03099e0b4dcc
|
25.2 MB | Download |
|
md5:ee354c058430b35836c3d26e026b5ac3
|
239.1 kB | Preview Download |
Additional details
Identifiers
Domain Specific Metadata
| Property | Value |
|---|---|
| Software | AMBER |
| Software Version | 2016 |
| Molecular Model | atomistic |
| Simulation Method | classical |
| Framestep | 0.01 nanoseconds |
| Length | 0.03 microseconds |
| Temperature | 300 K |
| Box Type | cubic |
| Trajectories | Cartesian coordinates |
| Force Fields | AMBER99 for DNA, parmBSC0, parmOL4, parmOL1 corrections for backbone dihedrals, TIP3P water. |
| Membrane | No |
| Sequences | TCTCTCTCTCTCTCTCACCACCGCGTACAAGAAAGTTTGTTCTTTCATTTCGCCATACAGCTGCCTCGCGCGTTTCGGTGATATCGGTGAAAACCCTTCCCGTTTCGCTCAAGTTAGTATAAAAAAGCTGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATACTGTAAAACACAACATATGCAGTCACTATGAATCAACTACTTAGATGGTATTAGTGACCTGTAACAGAGCTGAGGCATCTTTCTCAATGAAAGTGTCGGAACTCGGTACATAGGCTTCCGGCTGATAGTAGTCGTATACGACTACTATCAGCCGGAAGCCTATGTACCGAGTTCCGACACTTTCATTGAGAAAGATGCCTCAGCTCTGTTACAGGTCACTAATACCATCTAAGTAGTTGATTCATAGTGACTGCATATGTTGTGTTTTACAGTATTATGTAGTCTGTTTTTTATGCAAAATCTAATTTAATATATTGATATTTATATCATTTTACGTTTCTCGTTCAGCTTTTTTATACTAACTTGAGCGAAACGGGAAGGGTTTTCACCGATATCACCGAAACGCGCGAGGCAGCTGTATGGCGAAATGAAAGAACAAACTTTCTTGTACGCGGTGGTGAGAGAGAGAGAGAGA |
| Box Dimensions | 551.6 x 330.9 x 303.5 Angstrom, alpha: 90.0, beta: 90.0, gamma: 90.0 degrees |
| Long Range Cutoff | 100 Angstrom |
| Atom Count | 21564 |