[gmx-users] Problem: Protein move out of box

[Amit Choubey]

you can use trjconv -pbc nojump to take care of that.



On 10/8/09, Pan Wu <pan.wu at duke.edu> wrote:
> Hi Gromacs users,    I am new to Gromacs, and now setting up one very simple
> system to test Gromacs+Martini. (one protein with solvent surrounded)
>     When I run the MD and saw the trajectory, the protein seems go around
> randomly, and across the box size. Because Periodic Boundary Condition, it
> will come back from the other side. But I don't know *whether the across box
> size movement will actually cause some problem about protein structure or
> dynamics*?
>
>     In my mdout.mdp file, I can see:
>         comm-mode = Linear
>         nstcomm = 1
>         comm-grps  =                      (default, should be system)
>
>     Thank you in advance!
>
> Sincerely
> Pan
>
>
>
> --
> Sincerely
> =================================
> Pan Wu
> Graduate Student in Department of Chemistry
> Duke University
> 124 Science Drive
> 5301 French Family Science Center
> Durham, NC 27708
> Phone: (919) 660-1583
> =================================
>