[gmx-users] trjconv fit subset of atoms

[Joshua Adelman]

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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