加强 log
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@@ -52,12 +52,29 @@ echo "OUTPUT_FOLDER: $OUTPUT_FOLDER"
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echo "EXTRACT_EVERY_PS: $EXTRACT_EVERY_PS"
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echo "NUM_CORES: $NUM_CORES"
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# 函数：打印步骤信息和运行命令
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run_command() {
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local step_description=$1
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local command=$2
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echo "Starting: $step_description"
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echo "Command: $command"
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eval $command
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local status=$?
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if [ $status -ne 0 ]; then
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echo "Error in $step_description. Command: $command"
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exit $status
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fi
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echo "Completed: \n $step_description"
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}
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# generate GROMACS .gro file
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mpirun -np $NUM_CORES gmx_mpi pdb2gmx -f $NAME.pdb -o $NAME.gro -ff $FORCEFIELD -water $WATERMODEL -ignh -p topol.top
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run_command "Generating GROMACS .gro file" "mpirun -np $NUM_CORES gmx_mpi pdb2gmx -f $NAME.pdb -o $NAME.gro -ff $FORCEFIELD -water $WATERMODEL -ignh -p topol.top"
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# define the box
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mpirun -np $NUM_CORES gmx_mpi editconf -f $NAME.gro -o $NAME-box.gro -bt $BOXTYPE -c -d $BOXORIENTATION
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run_command "Defining the box" "mpirun -np $NUM_CORES gmx_mpi editconf -f $NAME.gro -o $NAME-box.gro -bt $BOXTYPE -c -d $BOXORIENTATION"
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# add solvate
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mpirun -np $NUM_CORES gmx_mpi solvate -cp $NAME-box.gro -cs $WATERTOPFILE -o $NAME-solv.gro -p topol.top
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run_command "Adding solvate" "mpirun -np $NUM_CORES gmx_mpi solvate -cp $NAME-box.gro -cs $WATERTOPFILE -o $NAME-solv.gro -p topol.top"
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# add icons # ! ions.mdp add by manual
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# --- ions.mdp file content --- #
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cat << EOF > ions.mdp
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@@ -76,9 +93,10 @@ rcoulomb = 1.0 ; Short-range electrostatic cut-off
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rvdw = 1.0 ; Short-range Van der Waals cut-off
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pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions
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EOF
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mpirun -np $NUM_CORES gmx_mpi grompp -f ions.mdp -c $NAME-solv.gro -p topol.top -o ions.tpr -maxwarn 1
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echo "SOL" > ions_input.txt
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mpirun -np $NUM_CORES gmx_mpi genion -s ions.tpr -o $NAME-solv-ions.gro -p topol.top -pname NA -nname CL -conc 0.125 -neutral < ions_input.txt
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run_command "Adding ions" "mpirun -np $NUM_CORES gmx_mpi grompp -f ions.mdp -c $NAME-solv.gro -p topol.top -o ions.tpr -maxwarn 1"
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# echo "SOL" > ions_input.txt
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# mpirun -np $NUM_CORES gmx_mpi genion -s ions.tpr -o $NAME-solv-ions.gro -p topol.top -pname NA -nname CL -conc 0.125 -neutral < ions_input.txt
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run_command "Generating ions" "echo 'SOL' | mpirun -np $NUM_CORES gmx_mpi genion -s ions.tpr -o $NAME-solv-ions.gro -p topol.top -pname NA -nname CL -conc 0.125 -neutral"
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# energy minimization of the structure in solvate # ! minim.mdp add by manual
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# --- minim.mdp file content --- #
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cat << EOF > minim.mdp
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@@ -97,8 +115,8 @@ rcoulomb = 1.0 ; Short-range electrostatic cut-off
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rvdw = 1.0 ; Short-range Van der Waals cut-off
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pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions
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EOF
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mpirun -np $NUM_CORES gmx_mpi grompp -f minim.mdp -c $NAME-solv-ions.gro -p topol.top -o em.tpr
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mpirun -np $NUM_CORES gmx_mpi mdrun -v -deffnm em
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run_command "Energy minimization" "mpirun -np $NUM_CORES gmx_mpi grompp -f minim.mdp -c $NAME-solv-ions.gro -p topol.top -o em.tpr"
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run_command "Running energy minimization" "mpirun -np $NUM_CORES gmx_mpi mdrun -v -deffnm em"
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# optional em, you will need the Xmgrace plotting too
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#gmx_mpi energy -f em.edr -o potential.xvg
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#position restrain
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@@ -150,8 +168,8 @@ gen_vel = yes ; assign velocities from Maxwell distributio
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gen_temp = 300 ; temperature for Maxwell distribution
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gen_seed = -1 ; generate a random seed
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EOF
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mpirun -np $NUM_CORES gmx_mpi grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr
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mpirun -np $NUM_CORES gmx_mpi mdrun -v -deffnm nvt
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run_command "Preparing NVT simulation" "mpirun -np $NUM_CORES gmx_mpi grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr"
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run_command "Running NVT simulation" "mpirun -np $NUM_CORES gmx_mpi mdrun -v -deffnm nvt"
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# optional : Let's analyze the temperature progression, again using energy:
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# gmx_mpi energy -f nvt.edr -o temperature.xvg
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# npt
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@@ -203,8 +221,8 @@ pbc = xyz ; 3-D PBC
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; Velocity generation
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gen_vel = no ; Velocity generation is off
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EOF
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mpirun -np $NUM_CORES gmx_mpi grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
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mpirun -np $NUM_CORES gmx_mpi mdrun -v -deffnm npt
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run_command "Preparing NPT simulation" "mpirun -np $NUM_CORES gmx_mpi grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr"
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run_command "Running NPT simulation" "mpirun -np $NUM_CORES gmx_mpi mdrun -v -deffnm npt"
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# Optional: Let's analyze the pressure progression, again using energy: type 18 0
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# gmx energy -f npt.edr -o pressure.xvg
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# Optional: Let's take a look at density as well, this time using energy and entering "24 0" at the prompt.
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@@ -261,8 +279,7 @@ gen_vel = no ; Velocity generation is off
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EOF
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# Generate GROMACS .tpr file for the simulation
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mpirun -np $NUM_CORES gmx_mpi grompp -f ${MDRUN_NAME}.mdp -c npt.gro -t npt.cpt -p topol.top -o ${TPR_FILE}
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run_command "Preparing MD simulation" "mpirun -np $NUM_CORES gmx_mpi grompp -f ${MDRUN_NAME}.mdp -c npt.gro -t npt.cpt -p topol.top -o ${TPR_FILE}"
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# Run the simulation
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mpirun -np $NUM_CORES gmx_mpi mdrun -deffnm ${MDRUN_NAME}
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# mpirun -np $(ls | egrep "Scaled[0-9]+$" | wc -l) gmx_mpi mdrun -v --deffnm md -cpi Scaled.cpt -multidir $(ls -v | egrep "Scaled[0-9]+$") -plumed plumed.dat -hrex -replex 1000 >& run_$(date "+%H%M%S_%d%m%Y").log || { echo "mdrun failed at line ${LINENO} "; exit -1; }
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@@ -270,44 +287,15 @@ mpirun -np $NUM_CORES gmx_mpi mdrun -deffnm ${MDRUN_NAME}
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echo -e "1\nq" | gmx_mpi make_ndx -f ${MDRUN_NAME}.gro -o ${NDX_FILE}
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# echo -e "1\nq" | gmx_mpi make_ndx -f md.gro -o index.ndx
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# Create extraction output directory
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mkdir -p ${OUTPUT_FOLDER}
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# Create extraction output directory Create temp output directory
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run_command "Creating output directories" "mkdir -p ${OUTPUT_FOLDER} && mkdir -p ${TEMP_FOLDER}"
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# Create temp output directory
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mkdir -p ${TEMP_FOLDER}
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echo -e "1\nq" | gmx_mpi trjconv -dt ${EXTRACT_EVERY_PS} -s ${TPR_FILE} -f ${XTC_FILE} -n ${NDX_FILE} -pbc mol -o ${TEMP_FOLDER}/temp.xtc
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# echo -e "1\nq" | gmx_mpi trjconv -dt 100 -s md.tpr -f md.xtc -n index.ndx -pbc mol -o temp/temp.xtc
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echo -e "1\n1\n1" | gmx_mpi trjconv -s ${TPR_FILE} -f ${TEMP_FOLDER}/temp.xtc -n ${NDX_FILE} -center -fit rot+trans -o ${TEMP_FOLDER}/traj_show.xtc
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# echo -e "1\n1\n1" | gmx_mpi trjconv -s md.tpr -f temp/temp.xtc -n index.ndx -center -fit rot+trans -o temp/traj_show.xtc
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echo -e "1\n1\n1" | gmx_mpi trjconv -s ${TPR_FILE} -f ${TEMP_FOLDER}/temp.xtc -n ${NDX_FILE} -center -fit rot+trans -b 0 -e 0 -o ${TEMP_FOLDER}/tarj_show.pdb
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# echo -e "1\n1\n1" | gmx_mpi trjconv -s md.tpr -f temp/temp.xtc -n index.ndx -center -fit rot+trans -b 0 -e 0 -o temp/tarj_show.pdb
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run_command "Extracting frames" "echo -e '1\nq' | gmx_mpi trjconv -dt ${EXTRACT_EVERY_PS} -s ${TPR_FILE} -f ${XTC_FILE} -n ${NDX_FILE} -pbc mol -o ${TEMP_FOLDER}/temp.xtc"
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run_command "Centering and fitting trajectory" "echo -e '1\n1\n1' | gmx_mpi trjconv -s ${TPR_FILE} -f ${TEMP_FOLDER}/temp.xtc -n ${NDX_FILE} -center -fit rot+trans -o ${TEMP_FOLDER}/traj_show.xtc"
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run_command "Generating PDB file" "echo -e '1\n1\n1' | gmx_mpi trjconv -s ${TPR_FILE} -f ${TEMP_FOLDER}/temp.xtc -n ${NDX_FILE} -center -fit rot+trans -b 0 -e 0 -o ${TEMP_FOLDER}/tarj_show.pdb"
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# Group 1 ( Protein)
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# ---
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# Step 1: Extract frames every 1000 ps
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gmx_mpi trjconv -s ${TPR_FILE} -f ${XTC_FILE} -o ${OUTPUT_FOLDER}/${NO_PBC_XTC_FILE} -dt ${EXTRACT_EVERY_PS} -pbc mol <<EOF
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0
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EOF
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# Step 2: Center and fit the trajectory
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# Centering the protein and fitting to the initial frame
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gmx_mpi trjconv -s ${TPR_FILE} -f ${OUTPUT_FOLDER}/${NO_PBC_XTC_FILE} -o ${OUTPUT_FOLDER}/${NO_PBC_XTC_FILE} -pbc mol -center <<EOF
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1
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1
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EOF
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# Step 3: Output PDB format file
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gmx_mpi trjconv -s ${TPR_FILE} -f ${OUTPUT_FOLDER}/${NO_PBC_XTC_FILE} -o ${OUTPUT_FOLDER}/${MDRUN_NAME}.pdb -pbc mol -center <<EOF
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1
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0
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EOF
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# Continue with further analysis like RMSD calculation...
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# ... [other analysis commands] ...
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@@ -317,7 +305,7 @@ EOF
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# command reference
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# Command 1: 提取蛋白质
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command_1 = f'echo "Protein" | gmx trjconv -dt 1000 -s {tpr_file} -f {xtc_file} -n {temp_folder}/tarj_show.ndx -pbc mol -o {temp_folder}/temp.xtc'
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# command_1 = f'echo "Protein" | gmx trjconv -dt 1000 -s {tpr_file} -f {xtc_file} -n {temp_folder}/tarj_show.ndx -pbc mol -o {temp_folder}/temp.xtc'
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# echo "Protein": 选择蛋白质组，用于告诉 gmx trjconv 要处理哪个部分。
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# -dt 1000: 指定时间间隔（这里是1000 picoseconds），用于从 .xtc 文件中抽取帧。
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# -s {tpr_file}: 指定拓扑文件（.tpr），它包含了模拟系统的完整描述。
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@@ -326,12 +314,12 @@ command_1 = f'echo "Protein" | gmx trjconv -dt 1000 -s {tpr_file} -f {xtc_file}
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# -pbc mol: 处理周期性边界条件，确保分子不会被分割。
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# -o {temp_folder}/temp.xtc: 指定输出文件名和位置。
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# Command 2: 中心对齐蛋白质
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command_2 = f'echo "Protein\nProtein\nProtein" | gmx trjconv -s {tpr_file} -f {temp_folder}/temp.xtc -n {temp_folder}/tarj_show.ndx -center -fit rot+trans -o {output_folder}/traj_show.xtc'
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# command_2 = f'echo "Protein\nProtein\nProtein" | gmx trjconv -s {tpr_file} -f {temp_folder}/temp.xtc -n {temp_folder}/tarj_show.ndx -center -fit rot+trans -o {output_folder}/traj_show.xtc'
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# echo "Protein\nProtein\nProtein": 三次选择蛋白质组，分别用于中心化、拟合和输出。
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# -center: 将蛋白质移动到框架的中心。
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# -fit rot+trans: 对齐蛋白质，通过旋转和平移来最佳拟合。
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# -o {output_folder}/traj_show.xtc: 指定输出文件名和位置。
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# Command 3: 抽取帧生成 .pdb 文件
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command_3 = f'echo "Protein\nProtein\nProtein" | gmx trjconv -s {tpr_file} -f {temp_folder}/temp.xtc -n {temp_folder}/tarj_show.ndx -center -fit rot+trans -b 0 -e 0 -o {output_folder}/tarj_show.pdb'
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# command_3 = f'echo "Protein\nProtein\nProtein" | gmx trjconv -s {tpr_file} -f {temp_folder}/temp.xtc -n {temp_folder}/tarj_show.ndx -center -fit rot+trans -b 0 -e 0 -o {output_folder}/tarj_show.pdb'
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# -b 0 -e 0: 指定开始和结束时间，这里设置为0表示只取第一帧。
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# -o {output_folder}/tarj_show.pdb: 输出为 .pdb 格式，存储在指定的位置。
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