/usr/share/votca/scripts/inverse/calc_density_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 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 | #! /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 calcs the density for gromacs for the AdResS therm force
Usage: ${0##*/}
EOF
exit 0
fi
sim_prog="$(csg_get_property cg.inverse.program)"
if [ "$sim_prog" = "gromacs" ]; then
topol=$(csg_get_property cg.inverse.gromacs.topol "topol.tpr")
[ -f "$topol" ] || die "${0##*/}: gromacs topol file '$topol' not found"
ext=$(csg_get_property cg.inverse.gromacs.traj_type "xtc")
traj="traj.${ext}"
[ -f "$traj" ] || die "${0##*/}: gromacs traj file '$traj' not found"
else
die "${0##*/}: Simulation program '$sim_prog' not supported yet"
fi
name=$(csg_get_interaction_property name)
max=$(csg_get_interaction_property tf.spline_end)
step=$(csg_get_interaction_property step)
bins=$(csg_calc $max / $step )
adress_type=$(get_simulation_setting adress_type)
echo "Adress type: $adress_type"
equi_time="$(csg_get_property cg.inverse.$sim_prog.equi_time 0)"
first_frame="$(csg_get_property cg.inverse.$sim_prog.first_frame 0)"
mol="$(csg_get_interaction_property tf.molname "*")"
if [ "$adress_type" = "sphere" ]; then
adressc="$(get_simulation_setting adress_reference_coords "0 0 0")"
ref="$(echo "$adressc" | awk '{if (NF<3) exit 1; printf "[%s,%s,%s]",$1,$2,$3;}')" || die "${0##*/}: we need three numbers in adress_reference_coords, but got '$adressc'"
axis="r"
opts="--ref $ref"
else
axis="x"
fi
msg "Calculating density for $name (molname $mol) on axis $axis"
if is_done "density_analysis-$name"; then
echo "density analysis is already done"
else
critical csg_density --trj "$traj" --top "$topol" --out "$name.dist.new" --begin "$equi_time" --first-frame "$first_frame" --rmax "$max" --bins "$bins" --axis "$axis" --molname "$mol" $opts
critical sed -i -e '/nan/d' -e '/inf/d' "$name.dist.new"
mark_done "density_analysis-$name"
fi
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