[gmx-users] trjconv fit subset of atoms

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Feb 26 20:13:06 CET 2009

Hi Josh,

When fitting, trjconv asks for separate groups for performing the fit
and for the output. No need to hack anything. You can make a suitable
index file using make_ndx.



On Thu, Feb 26, 2009 at 7:47 PM, Joshua Adelman <jadelman at berkeley.edu> wrote:
> 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
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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

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