[gmx-users] [Fwd: DNA separation]

[X.Periole]

On Sun, 21 May 2006 23:09:15 +0200
  Beniamino Sciacca <superbenji83 at yahoo.it> wrote:
> 
> 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.
> 

It seems that you are experiencing molecules jumping
over the periodic box !! You have the filter your 
trajectory
using trjconv and play wioth the options -pbc, may be
nojump, to view your system as a whole.

XAvier