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

shayamra at post.tau.ac.il shayamra at post.tau.ac.il
Sun Jul 4 00:45:04 CEST 2010

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.


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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