20 lines
879 B
Bash
Executable File
20 lines
879 B
Bash
Executable File
export GPU_ID="0"
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export NAME="protein"
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export LIGAND_GRO="mole.gro" # 配体的 .gro 文件
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export LIGAND_ITP="mole.itp" # 配体的 .itp 文件
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export FORCEFIELD=${FORCEFIELD:-"amber99sb"}
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export WATERMODEL=${WATERMODEL:-"tip3p"}
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export WATERTOPFILE=${WATERTOPFILE:-"spc216.gro"}
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export BOXTYPE=${BOXTYPE:-"tric"}
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export BOXORIENTATION=${BOXORIENTATION:-"1.0"}
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export NSTEPS=${NSTEPS:-50000000} # 100 ns 模拟
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export DT=${DT:-0.002} # 2 fs
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export MDRUN_NAME=${MDRUN_NAME:-"md"}
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export NDX_NAME=${NDX_NAME:-"index"}
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export TPR_FILE="${MDRUN_NAME}.tpr"
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export XTC_FILE="${MDRUN_NAME}.xtc"
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export NDX_FILE="${NDX_NAME}.ndx"
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export NO_PBC_XTC_FILE="${MDRUN_NAME}_noPBC.xtc"
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export OUTPUT_FOLDER=${OUTPUT_FOLDER:-"frame_extraction_output"}
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export TEMP_FOLDER=${TEMP_FOLDER:-"temp"}
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export EXTRACT_EVERY_PS=${EXTRACT_EVERY_PS:-100} # Default to 100 ps if not set |