[gmx-users] trajectory manipulation on individual groups or cut & paste ?

[Tsjerk Wassenaar]

Hi Marc,

What did you have in mind? I.e. what manipulations? I think you should
be able to do it using subsequent steps with trjconv, without
splitting the trajectory. Otherwise, it is trivial to make options
apply only to an index group, while writing everything out.

If, for example, you want to have a trajectory with the protein as a
whole (without jumps), and fitted to a reference, while the solvent is
arranged according to its smallest distance to the protein, it would
require three steps:

trjconv -pbc nojump
trjconv -ur molbox -pbc whole (my version)
trjconv -fit rot+trans

Hope it helps.

Cheers,

Tsjerk

On 8/3/05, David <spoel at xray.bmc.uu.se> wrote:
> On Wed, 2005-08-03 at 19:19 +0200, Marc Baaden wrote:
> > Hi,
> >
> > still manipulating and transforming trajectories. Actually the
> > options we need are all in trjconv, but the problem is that we
> > would need to apply them separately, either only to the protein(s)
> > or only to the water(s).
> >
> > Is this possible ?
> Don't think so...
> >
> > Or alternatively could one create separate protein and water trajectories,
> > manipulate them individually and then re-assemble into a common xtc file ?
> Yes, if you use an intermediate file like pdb and a script. Nothing more
> automatic I'm afraid...
> >
> > Thanks,
> >   Marc
> >
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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