[gmx-users] how to strip velocities out of a .gro file

Chris Neale chris.neale at utoronto.ca
Mon Jul 5 23:56:22 CEST 2010

Shay: that's a better idea than I had, thanks.

Tsjerk: that's likely as fast as its ever going to get. this is great. 
I was initially worried that it would mangle the last line of the .gro in a triclinic box definition, but it seems to be ok.

Thanks all,

-- original message --

What about:

find . -name "*.gro" -exec sed -i -e '$q' -e '3,$s/^\(.\{44\}.\).*$/\1/' {} \;

Assuming using a format %8.3f for coordinates and a single frame in
the .gro file. Otherwise things will get more complicated.



On Sun, Jul 4, 2010 at 12:45 AM,  <shayamra at post.tau.ac.il <http://lists.gromacs.org/mailman/listinfo/gmx-users>> wrote:
>/ How about:
/>/ 1. editconf -f file1.gro -o file1.pdb
/>/ 2. editconf -f file1.pdb -o file1_no_vel.gro
/>/ :-)
/>/ PDB contains just coordinates of atoms, so when you convert pdb to gro
/>/ again, you won't have the velocities.
/>/ Regards,
/>/ -Shay
/>/ Quoting chris.neale at utoronto.ca <http://lists.gromacs.org/mailman/listinfo/gmx-users>:
/>>/ If you have a directory full of .gro files that contain velocities, and if
/>>/ you don't need those velocities, then you're taking up too much space on
/>>/ your drive.
/>>/ It's too bad, but trjconv -novel -f in.gro -o out.gro will still write the
/>>/ velocities to out.gro.
/>>/ Here's a small script to strip the velocities out of a directory of .gro
/>>/ files. If anybody has a better idea of how to do this, then please post ;)
/>>/ #!/bin/bash
/>>/ for i in $(ls *.gro); do
/>>/  echo 0|trjconv -f $i -o a.xtc -novel -s $i;
/>>/  echo 0|trjconv -f a.xtc -novel -s $i -o a.gro;
/>>/  mv a.gro $i;
/>>/  rm a.xtc;
/>>/ done
/>>/ --
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