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

[Tsjerk Wassenaar]

Hi Chris,

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.

Cheers,

Tsjerk

On Sun, Jul 4, 2010 at 12:45 AM,  <shayamra at post.tau.ac.il> 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:
>
>> 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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>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands