[gmx-users] Question

Eric Smoll ericsmoll at gmail.com
Thu Oct 23 22:29:08 CEST 2014

Hello Gromacs users,

If I have all the files that were used to generate a trajectory file, what
is the proper procedure to update the atomnames in the trajectory. My best
guess is below. Is this problematic?

# remove first frame of trajectory
cat << EOF > tmp.ndx

trjconv -fr tmp.ndx -f old.trr -s old.tpr -o tmp.gro

# Edit tmp.gro and rename edit.gro

# Edit old.itp to edit.itp

# Edit old.top tp edit.top

grompp -f old.mdp -c edit.gro -p edit.top -o edit.tpr

trjconv -s edit.tpr -f old.trr -o new.trr

Thanks for the help!


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