[gmx-users] trjconv fit subset of atoms

[Tsjerk Wassenaar]

Josh,

-n indicates that groups are to be read from the index file, rather
than using the standard groups. It's not related to what the group is
being used for.

Cheers,

Tsjerk

On Thu, Feb 26, 2009 at 11:34 PM, Joshua Adelman <jadelman at berkeley.edu> wrote:
> I'm using 4.0.2. There are three optional ndx flags, -n -sub -fr. As far as
> I can tell, -n defines the output group (will also set the fit group as the
> same), -sub tells you the frame numbers for cutting the trajectory into
> smaller sections and -fr also has something to do with frames. If you don't
> define an .ndx file then it will ask you for a fit group, but what I want is
> to specify a particular set of atoms (not CA, backbone, etc).
> Maybe I'm just missing something simple. . . .
> Josh
>
>
>
>
> On Feb 26, 2009, at 11:12 AM, Berk Hess wrote:
>
> Hi,
>
> Which version of Gromacs are you using?
> In 4.0, but I think also in 3.3, trjconv ask for both a fit and an output
> group.
>
> Berk
>
> ________________________________
> To: gmx-users at gromacs.org
> From: jadelman at berkeley.edu
> Date: Thu, 26 Feb 2009 10:47:38 -0800
> Subject: [gmx-users] trjconv fit subset of atoms
>
> I am trying to use trjconv to generate a new .xtc file in which all frames
> have been aligned based on a subset of atoms (e.g. I have a multi-domain
> protein and I want to align the trajectory to one of the domains). Using a
> standard .ndx file only outputs the atoms associated with the fitted domain.
> I was wondering if there is a straightforward way to do what I describe
> without having to hack trjconv?
> Looking at the source for do_fit.c it looks like if I were to set the mass
> of atoms that I didn't want to use in the alignment to zero, then it might
> work, but I am generally trying to avoid having to generate a tpr file since
> I'm coming from the pdb/psf world.
> Any suggestions would be appreciated.
> Josh
>
> ------------------------------------------------------------------------------------------------------
> Joshua L. Adelman
> Biophysics Graduate Group              Lab: 510.643.2159
> 218 Wellman Hall                                Fax: 510.642.7428
> University of California, Berkeley     http://nature.berkeley.edu/~jadelman
> Berkeley, CA 94720 USA                   jadelman at berkeley.edu
> ------------------------------------------------------------------------------------------------------
>
>
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> ------------------------------------------------------------------------------------------------------
> Joshua L. Adelman
> Biophysics Graduate Group              Lab: 510.643.2159
> 218 Wellman Hall                                Fax: 510.642.7428
> University of California, Berkeley     http://nature.berkeley.edu/~jadelman
> Berkeley, CA 94720 USA                   jadelman at berkeley.edu
> ------------------------------------------------------------------------------------------------------
>
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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