[gmx-users] trajectory manipulation on individual groups or cut & paste ?
spoel at xray.bmc.uu.se
Thu Aug 4 13:52:00 CEST 2005
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.
> >>> 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 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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