[gmx-users] trjconv fit subset of atoms

[Joshua Adelman]

Ok, I think I see what's going on now. If I have two different groups  
in the ndx file, I can then select between them for the different  
purposes.

Sorry for the confusion.

Josh


On Feb 26, 2009, at 2:48 PM, Tsjerk Wassenaar wrote:

> 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
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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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