[gmx-users] [Fwd: DNA separation]

X.Periole X.Periole at rug.nl
Sun May 21 23:31:57 CEST 2006

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 

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


More information about the gromacs.org_gmx-users mailing list