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

[David]

On Thu, 2005-08-04 at 12:29 +0200, Marc Baaden wrote:
> Hi Tsjerk (and list)
> 
> so I finally compiled your modified trjconv version (using an older
> gmx 3.1.4 installation) and that solves indeed - at least for now -
> all my problems.
> 
> The actual problem was that the protein(s) (a long multi-chain system)
> were not kept together, one of the chains regularly jumped a boxlength
> to one direction. To correct this we used nojump, but this does ugly
> things to the water. So could we have applied nojump just to the protein
> (which probably just deserves a quick hack to trjconv using index groups
> as you pointed out) we could have done it with the standard trjconv in
> one go.
how about trjconv -pbc cluster

> 
> It is actually quite tricky to design the proper steps and options for
> trjconv in the right order :)  But that was finally (after a lot of
> trial and error) also possible.
> 
> Thanks,
> Marc
> 
> >>> Tsjerk Wassenaar said:
>  >> 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 trajectori
>      =
>  >> es,
>  >> > > manipulate them individually and then re-assemble into a common xtc fil
>      =
>  >> e ?
>  >> > 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
>  >> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>  >> >=20
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> 
> Marc Baaden
> 
-- 
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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