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cstein/center.sh

Created August 9, 2012 13:41
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How to center a molecule from an MD-simulation in Gromacs
Raw
center.sh
#!/usr/bin/env bash
TRAJIN=traj.xtc
TRAJOUT=trajfin.xtc
# delete the trajectory so gromacs wont display silly backup messages
if [ -e $TRAJOUT ]
then
rm -f $TRAJOUT
fi
# center molecule (you will be asked!)
trjconv -pbc mol -center -ur compact -s md.tpr -f $TRAJIN -o tmp.xtc
# make everything rotate and translate around that molecule (you will be asked!)
trjconv -fit rot+trans -s md.tpr -f tmp.xtc -o $TRAJOUT
rm -f tmp.xtc
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