[gmx-users] questions about remove PBC condition from trajectory

[Mark Abraham]

On 22/03/2015 12:19 pm, "凌未风" <grx1985 at qq.com> wrote:
>
> Hello, I have a trajectory and I have a problem to remove PBC condition.
> The problem is I have to small molecules in my system, and I would like
to put them in the same box (in the simulation, one of the molecule
diffused to another box, and I would like to remove this)

That's impossible. Think about the trajectory of one molecule from the
frame of reference of the other. It goes away on one side and comes back
from another.

Mark

> and keep them whole. I tried combination of the following two commands:
>
> 1, trjconv -f  input.xtc -o output.xtc -s xx.tpr -n index.ndx -pbc nojump
>  2, trjconv -f  input.xtc -o output.xtc -s xx.tpr -n index.ndx -pbc mol
>
> I also tried this:
> 1, trjconv -f  input.xtc -o output.xtc -s xx.tpr -n index.ndx -pbc nojump
>  2, trjconv -f  input.xtc -o output.xtc -s xx.tpr -n index.ndx -pbc whole
>
> However, I gound after command 1,  one of the molecule still diffused to
another box, and after command 2 the two molecules are put back into the
same box, but in some frames they are broken again.
> Dose anyone know how to put the two molecules in the same box (not let
one molecule diffuse to another box) and keep them whole molecules (not
broken)?
>
> I also tried a lot of other combinations, but none of them work. I really
appreciate your help. :)
>
> With my best regards,
> RXG
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