/usr/share/votca/scripts/inverse/initialize_step_generic_gromacs.sh is in votca-csg-scripts 1.2.4-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 | #! /bin/bash
#
# Copyright 2009-2011 The VOTCA Development Team (http://www.votca.org)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
if [[ $1 = "--help" ]]; then
cat <<EOF
${0##*/}, version %version%
This script implemtents the function initialize
Usage: ${0##*/}
Used external packages: gromacs
EOF
exit 0
fi
from="$(csg_get_property cg.inverse.initial_configuration "laststep")"
conf="$(csg_get_property cg.inverse.gromacs.conf "conf.gro")"
if [[ $from = "laststep" ]]; then
confout="$(csg_get_property cg.inverse.gromacs.conf_out "confout.gro")"
#avoid overwriting $confout
cp_from_last_step --rename "${confout}" "${conf}"
elif [[ $from = "maindir" ]]; then
cp_from_main_dir "$conf"
else
die "${0##*/}: initial_configuration '$from' not implemented"
fi
#convert potential in format for sim_prog
for_all non-bonded do_external convert_potential gromacs
check_temp || die "${0##*/}: check of tempertures failed"
if [[ $(csg_get_property cg.inverse.method) != "tf" ]]; then
for_all "non-bonded" check_cutoff || die "${0##*/}: check of cutoff for non-bonded interactions failed"
fi
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