脂質のCの密度分布をCの番号を変化させながら一度に計算するためのスクリプト

density_c.bash

#!/bin/bash

export GMX_MAXBACKUP=-1

function print_usage() {
    echo "${0} root_dir lipid_name"
    exit
}

if [ "$#" -ne 2 ]; then
    print_usage "${0}"
fi

# parse argument values
readonly IN_DIR="${1}"
readonly OUT_DIR="${1}/density"
readonly LIPID="${2}"

# create output directory
if [ ! -e "${OUT_DIR}" ]; then
    mkdir "${OUT_DIR}"
fi

function make_carbon_ndx() {
    c_pre=(3 2)
    eval local -a sn_c=$1
    local lipid0=$2
    local lipid1=$3
    for i in `seq 0 1`; do
        local ci="${c_pre[$i]}"
        for j in `seq 3 ${sn_c[$i]}`; do
            index="${OUT_DIR}/${lipid0}_c${ci}${j}.ndx"
            selstr="a C${ci}${j} & r ${lipid0}"
            gmx make_ndx -f "${IN_DIR}/step7_1.gro" -o ${index} <<EOF
del 0-4
r ${lipid0} | r ${lipid1}
${selstr}
q
EOF
            ./splitleafs/splitleafs.py -a ${lipid0}:P ${lipid1}:P --keep-residue -- "${IN_DIR}/step7_1.gro" >> ${index}
            gmx make_ndx -n ${index} -f "${IN_DIR}/step7_1.gro" -o ${index} <<EOF
1 & 3
1 & 2
q
EOF
        done
    done
}

function calc_density() {
    c_pre=(3 2)
    eval local -a sn_c=$1
    local lipid=$2
    for i in `seq 0 1`; do
        local ci="${c_pre[$i]}"
        for j in `seq 3 ${sn_c[$i]}`; do
            index="${OUT_DIR}/${lipid}_c${ci}${j}.ndx"
	          gmx density -f "${IN_DIR}/merged_trr/merged_tot.trr" -s "${IN_DIR}/step7_1.tpr" -relative -center -nosymm -dens number -d Z -n "${index}" -sl 400 -o "${OUT_DIR}/${lipid}_c${i}${j}_tot.xvg" <<EOF &
0
1
EOF
	          gmx density -f "${IN_DIR}/merged_trr/merged_tot.trr" -s "${IN_DIR}/step7_1.tpr" -relative -center -nosymm -dens number -d Z -n "${index}" -sl 400 -o "${OUT_DIR}/${lipid}_c${i}${j}_hi.xvg" <<EOF &
0
4
EOF
            gmx density -f "${IN_DIR}/merged_trr/merged_tot.trr" -s "${IN_DIR}/step7_1.tpr" -relative -center -nosymm -dens number -d Z -n "${index}" -sl 400 -o "${OUT_DIR}/${lipid}_c${i}${j}_lo.xvg" <<EOF &
0
5
EOF
        done
        wait
    done
    wait
}

sopc_cs=(18 18)
make_carbon_ndx "(${sopc_cs[*]})" "SOPC" "TSPC"
calc_density "(${sopc_cs[*]})" "SOPC"

tspc_cs=(32 18)
make_carbon_ndx "(${tspc_cs[*]})" "TSPC" "SOPC"
calc_density "(${tspc_cs[*]})" "TSPC"