[gmx-users] trajectory manipulation on individual groups or cut & paste ?
baaden at smplinux.de
Thu Aug 4 12:29:24 CEST 2005
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
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.
>> 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
>> > > 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
>> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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BioMolSim meeting 2&3 Sep 2005: http://www.iecb.u-bordeaux.fr/satellite2005/
Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
mailto:baaden at smplinux.de - http://www.baaden.ibpc.fr
FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217
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