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quick fix to test atomistic systems

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Robin
2025-08-11 23:11:35 +02:00
parent 93d0625ca6
commit 22e12c05d2
11 changed files with 3101 additions and 17 deletions
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13
create_annealing1.sh
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@@ -23,19 +23,18 @@ rm -r "$simdir" 2>/dev/null
mkdir "$simdir"
cp topology.top "$simdir/"
../replace_params.sh params.ini topology.top --output "$simdir/topology.top"
../replace_params.sh params_an1.ini mdp_parameters.mdp --output "$simdir/mdp_parameters.mdp"
../replace_params.sh params.ini "$simdir/mdp_parameters.mdp" --output "$simdir/mdp_parameters.mdp"
cp ../run.sh "$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" "$simdir/gro_start.gro"
annealing=$(../generate_annealing.py -d 50 -l 50 -u 1000 -s 100 -e 2000)
annealing=$($(dirname $0)/generate_annealing.py -d 50 -l 50 -u 1000 -s 50 -e 2000)
annealing=$(../generate_annealing.py -d 30 -l 400 -u 950 -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 = single" >> "$simdir/mdp_parameters.mdp"
echo "$annealing" >> "$simdir/mdp_parameters.mdp"