up version

create_annealing1.sh

@@ -1,40 +0,0 @@
-#!/bin/bash
-
-get_ini_value() {
-    local file=$1
-    local section=$2
-    local key=$3
-
-    awk -F '=' -v section="$section" -v key="$key" '
-    $0 ~ "\\[" section "\\]" { in_section = 1; next }
-    in_section && $1 ~ "^" key"[[:space:]]*$" {
-        gsub(/[[:space:]]+/, "", $2)
-        print $2
-        exit
-    }
-    $0 ~ /^\[/ { in_section = 0 }
-    ' "$file"
-}
-
-simdir="01_an1"
-
-
-rm -r "$simdir" 2>/dev/null
-mkdir "$simdir"
-
-cp topology.top "$simdir/"
-"$(dirname $0)/replace_params.sh" params.ini topology.top --output "$simdir/topology.top"
-"$(dirname $0)/replace_params.sh" params_an1.ini mdp_parameters.mdp --output "$simdir/mdp_parameters.mdp"
-"$(dirname $0)/replace_params.sh" params.ini "$simdir/mdp_parameters.mdp" --output "$simdir/mdp_parameters.mdp"
-cp "$(dirname $0)/run.sh" "$simdir/"
-cp "00_em/out/out.gro" "$simdir/gro_start.gro"
-
-
-annealing=$($(dirname $0)/generate_annealing.py -d 50 -l 50 -u 1000 -s 50 -e 2000)
-
-#annealing=$($(dirname $0)/generate_annealing.py -d 30 -l 400 -u 950 -s 50 -e 2000)
-
-echo "" >> "$simdir/mdp_parameters.mdp"
-echo "$annealing" >> "$simdir/mdp_parameters.mdp"
-
-

create_annealing2.sh

@@ -1,39 +0,0 @@
-#!/bin/bash
-
-get_ini_value() {
-    local file=$1
-    local section=$2
-    local key=$3
-
-    awk -F '=' -v section="$section" -v key="$key" '
-    $0 ~ "\\[" section "\\]" { in_section = 1; next }
-    in_section && $1 ~ "^" key"[[:space:]]*$" {
-        gsub(/[[:space:]]+/, "", $2)
-        print $2
-        exit
-    }
-    $0 ~ /^\[/ { in_section = 0 }
-    ' "$file"
-}
-
-simdir="02_an_cooling"
-
-
-rm -r "$simdir" 2>/dev/null
-mkdir "$simdir"
-
-cp topology.top "$simdir/"
-"$(dirname $0)/replace_params.sh" params.ini topology.top --output "$simdir/topology.top"
-"$(dirname $0)/replace_params.sh" params_an1.ini mdp_parameters.mdp --output "$simdir/mdp_parameters.mdp"
-"$(dirname $0)/replace_params.sh" params.ini "$simdir/mdp_parameters.mdp" --output "$simdir/mdp_parameters.mdp"
-cp "$(dirname $0)/run.sh" "$simdir/"
-#cp "00_em/out/out.gro" "$simdir/gro_start.gro"
-
-
-#annealing=$($(dirname $0)/generate_annealing.py -d 50 -l 180 -u 750 -e 2000 -c)
-annealing=$($(dirname $0)/generate_annealing.py -d 20 -l 750 -u 2100 -s 50 -e 10000 -c)
-
-echo "" >> "$simdir/mdp_parameters.mdp"
-echo "$annealing" >> "$simdir/mdp_parameters.mdp"
-
-

create_emin.sh

@@ -1,35 +0,0 @@
-#!/bin/bash
-
-get_ini_value() {
-    local file=$1
-    local section=$2
-    local key=$3
-
-    awk -F '=' -v section="$section" -v key="$key" '
-    $0 ~ "\\[" section "\\]" { in_section = 1; next }
-    in_section && $1 ~ "^" key"[[:space:]]*$" {
-        gsub(/[[:space:]]+/, "", $2)
-        print $2
-        exit
-    }
-    $0 ~ /^\[/ { in_section = 0 }
-    ' "$file"
-}
-
-
-simdir="00_em"
-
-
-rm -r "$simdir" 2>/dev/null
-mkdir "$simdir"
-
-cp topology.top "$simdir/"
-"$(dirname $0)/replace_params.sh" params.ini topology.top --output "$simdir/topology.top"
-"$(dirname $0)/replace_params.sh" params_emin.ini mdp_parameters.mdp --output "$simdir/mdp_parameters.mdp"
-"$(dirname $0)/replace_params.sh" params.ini "$simdir/mdp_parameters.mdp" --output "$simdir/mdp_parameters.mdp"
-cp "$(dirname $0)/run.sh" "$simdir/"
-cp "$(dirname $0)/templates/gro_$(get_ini_value params.ini params model).gro" "$simdir/gro_start.gro"
-
-echo "emstep                   = 0.001" >> $simdir/mdp_parameters.mdp
-
-

polyamorphism_optimization/annealing.py

@@ -0,0 +1,40 @@
+#!/usr/bin/env python3
+import shutil
+from pathlib import Path
+from generate_annealing import generate_annealing
+from replace_params import replace_params
+
+
+def main(root_dir: Path):
+    simdir = root_dir / "01_an1"
+
+    if simdir.exists():
+        shutil.rmtree(simdir)
+    simdir.mkdir()
+
+    # Copy topology and replace parameters
+    shutil.copy(root_dir / "topology.top", simdir / "topology.top")
+    replace_params(root_dir / "params.ini", root_dir / "topology.top", simdir / "topology.top")
+    replace_params(root_dir / "params_an1.ini", root_dir / "mdp_parameters.mdp", simdir / "mdp_parameters.mdp")
+    replace_params(root_dir / "params.ini", simdir / "mdp_parameters.mdp", simdir / "mdp_parameters.mdp")
+
+    # Copy run.sh
+    shutil.copy(root_dir / "run.sh", simdir / "run.sh")
+
+    # Generate annealing section
+    annealing = generate_annealing(d=50, l=50, u=1000, s=50, e=2000)
+    # -d 20 -l 750 -u 2100 -s 50 -e 10000 -c
+    with (simdir / "mdp_parameters.mdp").open("a") as f:
+        f.write("\n")
+        f.write(annealing)
+
+    print(f"Annealing directory {simdir} created and filled.")
+
+
+if __name__ == "__main__":
+    import sys
+    if len(sys.argv) != 2:
+        print(f"Usage: {sys.argv[0]} ROOT_DIRECTORY")
+        sys.exit(1)
+    main(Path(sys.argv[1]))
+

polyamorphism_optimization/emin.py

@@ -0,0 +1,36 @@
+#!/usr/bin/env python3
+import shutil
+from pathlib import Path
+from replace_params import replace_params
+
+
+def main(root_dir: Path):
+    simdir = root_dir / "00_em"
+
+    if simdir.exists():
+        shutil.rmtree(simdir)
+    simdir.mkdir()
+
+    # Copy topology and replace parameters
+    shutil.copy(root_dir / "topology.top", simdir / "topology.top")
+    replace_params(root_dir / "params.ini", root_dir / "topology.top", simdir / "topology.top")
+    replace_params(root_dir / "params_emin.ini", root_dir / "mdp_parameters.mdp", simdir / "mdp_parameters.mdp")
+    replace_params(root_dir / "params.ini", simdir / "mdp_parameters.mdp", simdir / "mdp_parameters.mdp")
+
+    # Copy run.sh
+    shutil.copy(root_dir / "run.sh", simdir / "run.sh")
+
+    # Add finer emstep
+    with (simdir / "mdp_parameters.mdp").open("a") as f:
+        f.write("\n")
+        f.write("emstep                   = 0.001")
+
+    print(f"Energy minimization directory {simdir} created and filled.")
+
+
+if __name__ == "__main__":
+    import sys
+    if len(sys.argv) != 2:
+        print(f"Usage: {sys.argv[0]} ROOT_DIRECTORY")
+        sys.exit(1)
+    main(Path(sys.argv[1]))

polyamorphism_optimization/initialize_sim.py

@@ -0,0 +1,46 @@
+#!/usr/bin/env python3
+import argparse
+import os
+import subprocess
+from pathlib import Path
+from importlib.resources import files
+import configparser
+
+from annealing import main as annealing
+from emin import main as emin
+
+
+# --- Core function ---
+def initialize_simulation_dir(directory: Path):
+    os.chdir(directory)
+    
+    params = configparser.ConfigParser()
+    params = params.read('params.ini')
+
+    template_path = files("polyamorphism_optimization.templates") / f"topology_{params['model']}.top"
+    TOPOLOGY = template_path.read_text()
+    template_path = files("polyamorphism_optimization.templates") / "mdp_parameters.mdp"
+    MDP_PARAMETERS = template_path.read_text()
+    
+    # Write files
+    Path("mdp_parameters.mdp").write_text(MDP_PARAMETERS)
+    Path("topology.top").write_text(TOPOLOGY)
+
+    emin(directory)
+    annealing(directory)
+
+    print(f"finished and simulation directory {directory} created and filled")
+    for f in os.listdir(directory):
+        print(f)
+
+# --- CLI entry point ---
+def main():
+    parser = argparse.ArgumentParser(description="Create simulation input files.")
+    parser.add_argument("-d", "--directory", default=".", help="Base directory")
+    args = parser.parse_args()
+
+    create_simulation_dir(Path(args.directory))
+
+if __name__ == "__main__":
+    main()
+

polyamorphism_optimization/replace_params.py

@@ -0,0 +1,41 @@
+#!/usr/bin/env python3
+import sys
+import configparser
+from pathlib import Path
+
+
+def replace_params(param_file: Path, template_file: Path, output_file: Path):
+    """Replace placeholders in template_file with values from an INI file."""
+    config = configparser.ConfigParser()
+    config.optionxform = str  # keep case sensitivity
+    config.read(param_file)
+
+    # Flatten into a simple dict {KEY: VALUE}
+    params = {}
+    for section in config.sections():
+        for key, value in config.items(section):
+            params[key] = value
+
+    content = template_file.read_text()
+
+    for key, value in params.items():
+        content = content.replace(key, value)
+
+    output_file.write_text(content)
+
+
+def main():
+    if len(sys.argv) != 4:
+        print(f"Usage: {sys.argv[0]} PARAM_FILE TEMPLATE_FILE OUTPUT_FILE")
+        sys.exit(1)
+
+    param_file = Path(sys.argv[1])
+    template_file = Path(sys.argv[2])
+    output_file = Path(sys.argv[3])
+
+    replace_params(param_file, template_file, output_file)
+
+
+if __name__ == "__main__":
+    main()
+

polyamorphism_optimization/templates/NPT.ini

@@ -0,0 +1,9 @@
+INTEGRATOR = md
+NSTEPS = 2000000
+NLOG = 1000
+NENERGY = 100
+NSTXOUT = 1000
+TCOUPL = v-rescale
+TAUT = 1.0
+PCOUPL = c-rescale
+TAUP = 1.0

polyamorphism_optimization/templates/NVT.ini

@@ -0,0 +1,9 @@
+INTEGRATOR = md
+NSTEPS = 2000000
+NLOG = 1000
+NENERGY = 100
+NSTXOUT = 1000
+TCOUPL = v-rescale
+TAUT = 1.0
+PCOUPL = no
+TAUP = 1.0

polyamorphism_optimization/templates/mdp_parameters.mdp

@@ -0,0 +1,31 @@
+integrator               =  INTEGRATOR
+dt                       = 0.001
+nsteps                   =  NSTEPS
+nstcomm                  = 10
+nstlog                   =  NLOG
+nstcalcenergy            = 10
+nstenergy                =  NENERGY
+nstxout-compressed       =  NSTXOUT
+compressed-x-precision   = 1000
+energygrps               = system
+rlist                    = 1.2
+nstlist                  = 10
+coulombtype              = pme
+rcoulomb                 = 1.2
+coulomb-modifier         = potential-shift-verlet
+vdwtype                  = pme
+rvdw                     = 1.2
+vdw-modifier             = potential-shift-verlet
+fourierspacing           = 0.144
+tcoupl                   = v-rescale
+tau_t                    =  TAUT
+gen_vel                  = yes
+gen_temp                 =  TEMP
+ref_t                    =  TEMP
+tc-grps                  = system
+pcoupl                   =  PCOUPL
+tau_p                    =  TAUP
+ref_p                    =  PRESSURE
+compressibility          = 4.5e-5
+nstpcouple               = 10
+nsttcouple               = 10

polyamorphism_optimization/templates/params/annealing1.ini

@@ -0,0 +1,10 @@
+INTEGRATOR = md
+NSTEPS = 2000000
+NLOG = 1000
+NENERGY = 100
+NSTXOUT = 1000
+TCOUPL = v-rescale
+TAUT = 0.5
+TEMP = 10.0
+PCOUPL = c-rescale
+TAUP = 1.0

polyamorphism_optimization/templates/params/annealing2.ini

@@ -0,0 +1,10 @@
+INTEGRATOR = md
+NSTEPS = 5000000
+NLOG = 1000
+NENERGY = 100
+NSTXOUT = 1000
+TCOUPL = v-rescale
+TAUT = 0.5
+TEMP = 10.0
+PCOUPL = c-rescale
+TAUP = 1.0

polyamorphism_optimization/templates/params/emin.ini

@@ -0,0 +1,10 @@
+INTEGRATOR = steep
+NSTEPS = 10000
+NLOG = 100
+NENERGY = 100
+NSTXOUT = 100
+TAUT = 1.0
+TEMP = 300
+PCOUPL = no
+TCOUPL = no
+TAUP = 1.0

polyamorphism_optimization/templates/run.sh

@@ -4,17 +4,18 @@
 #SBATCH --ntasks=1
 #SBATCH --cpus-per-task=8
 #SBATCH --gres=gpu:1
-#SBATCH --exclude=linux-05,linux-08,linux-02,linux-03,linux-04,linux-07
+##SBATCH --exclude=linux-05,linux-06,linux-07,linux-08
 
-#if [ "$(gmx --version | grep "GROMACS version")" != GROMACS*2025.2* ] ; then
-#    echo "Version loaded is not 2025.2! Exiting!"
+#if [ "$(gmx --version | grep "GROMACS version")" != GROMACS*2023.3* ] ; then
+#    echo "Version loaded is not 2023.3! Exiting!"
 #    exit 1
 #fi
 
+PHYS_CORES=$(lscpu | awk -F: '/Core\(s\) per socket/ {print $2+0}')
 if [ -n "$SLURM_CPUS_PER_TASK" ]; then
     NT="-nt $SLURM_CPUS_PER_TASK"
-elif [ $(nproc) -lt 9 ] ; then
-    NT="-nt $(nproc)"
+elif [ "$PHYS_CORES" -lt 9 ] ; then
+    NT="-nt $PHYS_CORES"
 else
     NT="-nt 8"
 fi
@@ -29,7 +30,7 @@ mkdir -p "$WORKDIR/out"
 export GMX_MAXCONSTRWARN=-1;
 gmx -nobackup grompp \
     -f $WORKDIR/mdp_parameters.mdp \
-    -o $WORKDIR/tpr_run.tpr \
+    -o $WORKDIR/out/tpr_run.tpr \
     -c $WORKDIR/gro_start.gro \
     -r $WORKDIR/gro_start.gro \
     -p $WORKDIR/topology.top \
@@ -42,7 +43,7 @@ if [ $? != 0 ] ; then
 fi
 
 gmx mdrun \
-    -s $WORKDIR/tpr_run.tpr \
+    -s $WORKDIR/out/tpr_run.tpr \
     -o $WORKDIR/out/trr_traj.trr \
     -c $WORKDIR/out/out.gro \
     -x $WORKDIR/out/xtc_traj.xtc \

polyamorphism_optimization/templates/top_3point.top

@@ -0,0 +1,33 @@
+[ defaults ]
+; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
+  1             2               yes              1.0     1.0
+[atomtypes]
+;name     mass      charge   ptype    sigma        epsilon
+A     MASS       0.000       A      SIGMA_A         EPSILON_A
+B     MASS       0.000       A      SIGMA_B         EPSILON_B
+
+[moleculetype]
+; name nrexcl
+L  1
+
+[atoms]
+; nr type resnr residu atom cgnr charge
+1     A   1     L  A    1    CHARGE_A      MASS 
+2     B   1     L  B1   1    CHARGE_B      MASS 
+3     B   1     L  B2   1    CHARGE_B      MASS 
+
+[settles]
+;i      funct   doh     dhh
+1       1       D_AB     D_BB 
+
+
+[exclusions]
+1       2       3
+2       1       3
+3       1       2
+
+[system]
+ MODEL 
+
+[molecules]
+L                 NMOL 

polyamorphism_optimization/templates/top_4point.top

@@ -0,0 +1,40 @@
+[ defaults ]
+; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
+  1             2               yes              1.0     1.0
+[atomtypes]
+;name     mass      charge   ptype    sigma        epsilon
+A     MASS       0.000       A      SIGMA_A         EPSILON_A
+B     MASS       0.000       A      SIGMA_B         EPSILON_B
+D     0          0.000       D   0.0           0.0
+
+[moleculetype]
+; name nrexcl
+L  1
+
+[atoms]
+; nr type resnr residu atom cgnr charge
+1     A   1     L  A    1     0        MASS 
+2     B   1     L  B1   1    CHARGE_B      MASS 
+3     B   1     L  B2   1    CHARGE_B      MASS 
+4     D   1     L  D    1    CHARGE_A      0.0
+
+[settles]
+;i      funct   doh     dhh
+1       1       D_AB     D_BB 
+
+
+[dummies3]
+; Dummy from                            funct       a        b
+4       1       2       3       1       DUMMY_AB      DUMMY_AB 
+
+[exclusions]
+1       2       3       4
+2       1       3       4
+3       1       2       4
+4       1       2       3
+
+[system]
+ MODEL 
+
+[molecules]
+L                 NMOL 

polyamorphism_optimization/templates/top_atomistic.top

@@ -0,0 +1,31 @@
+[ defaults ]
+; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
+  1             2               yes              1.0     1.0
+
+[atomtypes]
+;name     mass      charge   ptype    sigma        epsilon
+A     MASS       0.000       A      SIGMA_A         EPSILON_A 
+B     MASS       0.000       A      SIGMA_B         EPSILON_B 
+
+[moleculetype]
+; name nrexcl
+A  1
+
+[atoms]
+; nr type resnr residu atom cgnr charge
+1     A   1     L  A   1    CHARGE_A      MASS 
+
+[moleculetype]
+; name nrexcl
+B  1
+
+[atoms]
+; nr type resnr residu atom cgnr charge
+1     B   1     L  B   1    CHARGE_B      MASS 
+
+[system]
+ MODEL 
+
+[molecules]
+A                NMOL
+B                NMOLB

pyproject.toml

@@ -0,0 +1,24 @@
+[build-system]
+requires = ["setuptools>=80.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "polyamorphism_optimization"
+version = "0.2.0"
+requires-python = ">=3.12"
+
+dependencies = [
+    "pip>=25",
+    "wheel>=0.45",
+    "numpy>=2.3",
+    "scipy>=1.16",
+    "pandas>=2.3",
+    "mdevaluate @ git+ssh://git@gitea.pkm.physik.tu-darmstadt.de/IPKM/mdevaluate.git@feature/compatibility_robin",
+]
+
+[project.scripts]
+po_init_sim = "polyamorphism_optimization.initialize_sim:main"
+
+[tool.setuptools.package-data]
+polyamorphism_optimization = ["templates/*"]
+

replace_params.sh

@@ -1,47 +0,0 @@
-#!/usr/bin/env bash
-
-set -e
-
-if [[ $# -lt 2 ]]; then
-    echo "Usage: $0 <params.ini> <template> [--output <output_file>]"
-    exit 1
-fi
-
-PARAMS_FILE="$1"
-TEMPLATE_FILE="$2"
-OUTPUT_FILE="${TEMPLATE_FILE}.out"
-
-# Optional --output <filename>
-if [[ "$3" == "--output" && -n "$4" ]]; then
-    OUTPUT_FILE="$4"
-fi
-
-declare -A PARAMS
-
-# Load params.ini (ignore [section] headers)
-while IFS='=' read -r key value; do
-    # Trim whitespace and ignore comments/sections
-    key="${key%%\#*}"   # remove inline comments
-    value="${value%%\#*}"
-    key="$(echo "$key" | xargs)"     # trim leading/trailing whitespace
-    value="$(echo "$value" | xargs)"
-    [[ -z "$key" || "$key" =~ ^\[.*\]$ ]] && continue
-
-    key_upper=$(echo "$key" | tr '[:lower:]' '[:upper:]')
-    PARAMS["$key_upper"]="$value"
-done < "$PARAMS_FILE"
-
-# Read template into a variable
-template=$(<"$TEMPLATE_FILE")
-
-# Replace placeholders (only when surrounded by spaces)
-for key in "${!PARAMS[@]}"; do
-    val="${PARAMS[$key]}"
-    # Use sed to do space-surrounded substitution
-    template=$(echo "$template" | sed -E "s/([[:space:]])$key([[:space:]])/$val/g")
-done
-
-# Save to output file
-echo "$template" > "$OUTPUT_FILE"
-echo "Wrote output to $OUTPUT_FILE"
-

setup_env.sh

@@ -0,0 +1,6 @@
+python3.12 -m venv .venv
+source .venv/bin/activate
+pip install -e .
+rm -r *egg-info
+# pip install --upgrade --force-reinstall .
+

setup_sim.sh

@@ -1,182 +0,0 @@
-#!/bin/bash -l
-
-usage() { echo "Usage: $0 [-d basedirectory ]" 1>&2; exit 1; }
-
-DIRECTORY="."
-
-while getopts "d:" opt; do
-  case $opt in
-    d )
-        DIRECTORY=$OPTARG
-        ;;
-    h )
-        usage
-        ;;
-   \? )
-        usage
-        ;;
-  esac
-done
-
-cd $DIRECTORY
-
-#=====================================================================================
-cat > mdp_parameters.mdp << EOF
-integrator               =  INTEGRATOR 
-dt                       = 0.001
-nsteps                   =  NSTEPS 
-nstcomm                  = 10
-
-nstlog                   =  NLOG 
-nstcalcenergy            = 10
-nstenergy                =  NENERGY 
-nstxout-compressed       =  NSTXOUT 
-compressed-x-precision   = 1000
-energygrps               = system
-
-rlist                    = 1.2
-nstlist                  = 10
-
-coulombtype              = pme
-rcoulomb                 = 1.2
-coulomb-modifier         = potential-shift-verlet
-vdwtype                  = pme
-rvdw                     = 1.2
-vdw-modifier             = potential-shift-verlet
-fourierspacing           = 0.144
-
-tcoupl                   = v-rescale
-tau_t                    =  TAUT 
-gen_vel                  = yes
-gen_temp                 =  TEMP 
-ref_t                    =  TEMP 
-tc-grps                  = system
-
-pcoupl                   =  PCOUPL 
-tau_p                    =  TAUP 
-ref_p                    =  PRESSURE 
-compressibility          = 4.5e-5
-
-nstpcouple               = 10
-nsttcouple               = 10
-
-EOF
-
-#=====================================================================================
-cat > params_emin.ini << EOF
-INTEGRATOR = steep
-NSTEPS = 10000
-NLOG = 100
-NENERGY = 100
-NSTXOUT = 100
-TAUT = 1.0
-TEMP = 300
-PCOUPL = no
-TCOUPL = no
-TAUP = 1.0
-EOF
-
-cat > params_an1.ini << EOF
-INTEGRATOR = md
-NSTEPS = 2000000
-NLOG = 1000
-NENERGY = 100
-NSTXOUT = 1000
-TCOUPL = v-rescale
-TAUT = 0.5
-TEMP = 10.0
-PCOUPL = c-rescale
-TAUP = 1.0
-EOF
-
-#=====================================================================================
-
-cat > topology.top << EOF
-[ defaults ]
-; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
-  1             2               yes              1.0     1.0
-
-[atomtypes]
-;name     mass      charge   ptype    sigma        epsilon
-A     MASS       0.000       A      SIGMA_A         EPSILON_A 
-B     MASS       0.000       A      SIGMA_B         EPSILON_B 
-D     0             0.000       D   0.0           0.0
-
-[moleculetype]
-; name nrexcl
-L  1
-
-[atoms]
-; nr type resnr residu atom cgnr charge
-1     A   1     L  A    1     0        MASS 
-2     B   1     L  B1   1    CHARGE_B      MASS 
-3     B   1     L  B2   1    CHARGE_B      MASS 
-4     D   1     L  D    1    CHARGE_A      0.0
-
-[settles]
-;i      funct   doh     dhh
-1       1       D_AB     D_BB 
-
-
-[dummies3]
-; Dummy from                            funct       a        b
-4       1       2       3       1       DUMMY_AB      DUMMY_AB 
-
-[exclusions]
-1       2       3       4
-2       1       3       4
-3       1       2       4
-4       1       2       3
-
-[system]
- MODEL 
-
-[molecules]
-L                 NMOL 
-EOF
-
-cat > topology.top << EOF
-[ defaults ]
-; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
-  1             2               yes              1.0     1.0
-
-[atomtypes]
-;name     mass      charge   ptype    sigma        epsilon
-A     MASS       0.000       A      SIGMA_A         EPSILON_A 
-B     MASS       0.000       A      SIGMA_B         EPSILON_B 
-
-[moleculetype]
-; name nrexcl
-A  1
-
-[atoms]
-; nr type resnr residu atom cgnr charge
-1     A   1     L  A   1    CHARGE_A      MASS 
-
-[moleculetype]
-; name nrexcl
-B  1
-
-[atoms]
-; nr type resnr residu atom cgnr charge
-1     B   1     L  B   1    CHARGE_B      MASS 
-
-[system]
- MODEL 
-
-[molecules]
-A                1000
-B                2000
-EOF
-
-#=====================================================================================
-echo $(dirname $0)
-bash ".$(dirname $0)/create_emin.sh"
-bash ".$(dirname $0)/create_annealing1.sh"
-
-
-#=====================================================================================
-
-echo "finished and simulation directory $DIRECTORY created and filled"
-ls
-exit 0