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, <shaya...@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.ne...@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 >> >> -- >> gmx-users mailing list gmx-us...@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use thewww interface >> or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php