[gmx-users] trjconv - two chains are separated

[Catarina A. Carvalheda dos Santos]

Hi there,

I had similar problems in the past. You'll have to play with trjconv and
find the best combination of different flags to solve the visualization
problem.

You can start by trying out this workflow for example:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Hope this helps.

Good luck!



On 3 February 2016 at 06:15, Trayder Thomas <trayder.thomas at monash.edu>
wrote:

> 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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-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
SLS & SSE
University of Dundee
DD1 5EH, Dundee, Scotland, UK