[gmx-users] trjconv - two chains are separated

[Trayder Thomas]

For "-pbc nojump" to work, you need to make sure they are together (as you
want) in the first frame of your input trajectory.

The most reliable way to do this is by centering the trajectory on a
residue at the interface between the two chains (using a custom index
group).

I've also heard some people have had luck with "-pbc cluster"

You can then run "-pbc nojump" on the centered (or clustered) trajectory.

-Trayder




On Wed, Feb 3, 2016 at 9:37 AM, Yunlong Liu <yliu120 at jh.edu> wrote:

> Hi Gromacs Users,
>
> I used "gmx trjconv" (Gromacs 5.0.4) to remove the pbc of my trajectories.
> My protein has two chains (A and B) and they closely bind to each other.
> after running trjconv with "-pbc nojump", two chains are greatly separated
> by a certain distance. It is mostly likely that the pbc is not successfully
> removed and the program takes a chain from one unit cell and another from
> another unit cell.
>
> Does anybody have any idea to solve the problem?
>
> Best
> Yunlong
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