[gmx-users] how to write a frames.ndx for -fr option of trjconv

Justin A. Lemkul jalemkul at vt.edu
Fri Jul 16 13:05:48 CEST 2010

Hassan Shallal wrote:
> Dear Gromacs users,
> I need trjconv to write me pdb files at a list of frames that are 
> randomly chosen throughout the whole production trajectory (they belong 
> to the least energetic 100 frames).
> I can use trjconv to write a pdb at each frame but this is gonna be time 
> consuming, so I looked in the specifications of trjconv and found that
> there is an optional input -fr frames.ndx, I guess this might be useful 
> for what I want but I am not quite sure how to write an index file for 
> randomly distributed frames points not
> for atoms or residues, the command make_ndx doesn;t provide any options 
> for frames of time points!!
> I tried to create an ndx file manually by writing the frames numbers in 
> a txt file, calling it frames.ndx,  feed this to the -fr option of 
> trjconv, as I expected, trjconv dealt with
> the numbers as numbers of atoms not of frames! How can I tell trjconv 
> that the numbers in frames.ndx file are actually numbers of specific 
> time points not of residues.

That's what it's supposed to do, so I'd suspect that there's something wrong 
with your index file.  If you want to write out frames 1 and 2, for instance, 
your frames.ndx file should be something like:

[ frames ]
   1  2


> Any help or hint is very appreciated..
> Thanks alot
> Hassan


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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