[gmx-users] how to write a frames.ndx for -fr option of trjconv
hshallal at PACIFIC.EDU
Fri Jul 16 10:22:23 CEST 2010
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.
Any help or hint is very appreciated..
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