[gmx-users] Removing PBC from Replica Exchange Trajectory

[Tsjerk Wassenaar]

Hi Robert,

Maybe it's a bit nasty, but you may try the following, assuming that
your ends stay a bit together:

1. Translate your system such that the last atom of chain A is
centered in the _rectangular_ unitcell.
2. Generate a .tpr file from the translated system
3. Convert the .tpr to .pdb

Gromacs places molecules in the box based on the first atom. Since
you're dealing with DNA, your chains will be head to tail. Placing the
tail of chain A in the center would mean that there's a periodic image
of your chain B which has its first atom in the center. This image
will be chosen during the generation of the .tpr file. Converting the
.tpr to .pdb should give both chains close to each other. Processing
the trajectory will be another thing...

Tsjerk


On 3/15/07, Robert Johnson <bobjohnson1981 at gmail.com> wrote:
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623