[gmx-users] Removing PBC from Replica Exchange Trajectory

[Robert Johnson]

I made an index file that contained the middle portion of the DNA
strand. I then used the -center option to center this middle portion
in the box and then outputted the entire molecule. However, the
molecule still appears broken. What is this -pbc mol option? That
doesn't seem to be one of the available pbc options.
Bob

On 3/14/07, Yang Ye <leafyoung81-group at yahoo.com> wrote:
> A rather simple but effective way is to make an index which contains 1/4
> of your protein file. Use trjconv with -center tric -pbc whole/mol to
> center that 1/4 of your protein and output the whole protein.
>
>
> Tsjerk Wassenaar wrote:
> > Hi Bob,
> >
> > You could try -pbc cluster. If that doesn't work, it'll be difficult.
> > The option -pbc nojump will only work on continuous trajectories.
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On 3/14/07, Robert Johnson <bobjohnson1981 at gmail.com> wrote:
> >> Hello everyone,
> >> I'm trying to visualze the conformations of a ssDNA molecule obtained
> >> from a
> >> REMD trajectory. As expected, there are parts of the simulation where
> >> the
> >> oligomer is broken due to the PBC wrapping. I've been trying to fix
> >> this with
> >> trjconv. However, the -pbc nojump option doesn't work - it actually
> >> makes the
> >> broken portions of the molecule worse and gives a terribly distorted
> >> trajectory. Since the REMD trajectory isn't continuous (i.e. there are
> >> instaneous jumps in the coordinates associated with REMD swaps), the
> >> nojump
> >> option may have problems. Does anyone know of any other way or other
> >> tools that
> >> I could use to reassemble my broken DNA strand?
> >> Thanks,
> >> Bob Johnson
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