[gmx-users] [Fwd: DNA separation]

[Beniamino Sciacca]

Dear community,
I've a problem during the MD of a double strand molecule of DNA.
I worked with heavy H and virtual site.
I minimized in vacuum, then i solvated and minimezed.
Later I've heated (simulated annealing) for 50 ps.
Then I simulated 1200 ps of MD.
There has not been any crash.
Viewing RMSD, in 4 point there is a peak.
Viewing, with VMD, the dinamic in the same steps the molecule is 
separated in 2 molecule single strand; the next step the molecule return 
in double strand configuration and the dinamic continue without any problem.

I attach .xvg and .mdp file of the dinamic.

I thank you in advance  for your answer
Beniamino Sciacca


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