GROMACS_ANALYZE_dihedral_analysis

# ff=oplsaa
ff=cgenff
# ff=ligpargen

cd /gem/iorga/repositories/2020-SAMPL7-PhysProp/03_logP_mdpow/sims/_dih_analysis

for i in `ls -1d /gem/iorga/repositories/2020-SAMPL7-PhysProp/03_logP_mdpow/sims/$ff/SM46/SM46/FEP/*/*/* | grep -v 'extended'`; do

  # echo $i
  j=`echo $i | tr '/' '-' | sed 's/.*sims-//g' | sed 's/SM46-SM46-FEP/SM46/g'`
  echo $j
  gmx angle -type dihedral -f $i/md.xtc -n $ff-dih1.ndx -od $j-dih1-dist.xvg -ov $j-dih1-ts.xvg
  gmx angle -type dihedral -f $i/md.xtc -n $ff-dih2.ndx -od $j-dih2-dist.xvg -ov $j-dih2-ts.xvg

done