update gromacs script

md_gromacs.sh

@@ -20,14 +20,17 @@ DT=${DT:-0.002} # 2 fs
 #BOXCENTER="2.5"
 # Define simulation name variable
 MDRUN_NAME=${MDRUN_NAME:-"md"}
+NDX_NAME=${NDX_NAME:-"index"}
 # Define analysis parameters
 # Define other filenames based on MDRUN_NAME
 TPR_FILE="${MDRUN_NAME}.tpr"
 XTC_FILE="${MDRUN_NAME}.xtc"
+NDX_FILE="${NDX_NAME}.ndx"
 NO_PBC_XTC_FILE="${MDRUN_NAME}_noPBC.xtc"
-OUTPUT_FOLDER=${OUTPUT_FOLDER:-"analysis_results"}
+OUTPUT_FOLDER=${OUTPUT_FOLDER:-"frame_extraction_output"}
+TEMP_FOLDER=${TEMP_FOLDER:-"temp"}
 # Define variables for frame extraction
-EXTRACT_EVERY_PS=${EXTRACT_EVERY_PS:-1000} # Default to 1000 ps if not set
+EXTRACT_EVERY_PS=${EXTRACT_EVERY_PS:-100} # Default to 100 ps if not set
 
 # Print the current settings
 echo "Current settings:"
@@ -204,7 +207,7 @@ gmx_mpi mdrun -v -deffnm npt
 # gmx energy -f npt.edr -o density.xvg
 # md
 # --- md.mdp file content --- #
-cat << EOF > md.mdp
+cat << EOF > ${MDRUN_NAME}.mdp
 title                   = OPLS Lysozyme NPT equilibration
 ; Run parameters
 integrator              = md        ; leap-frog integrator
@@ -258,10 +261,57 @@ gmx_mpi grompp -f ${MDRUN_NAME}.mdp -c npt.gro -t npt.cpt -p topol.top -o ${TPR_
 
 # Run the simulation
 gmx_mpi mdrun -deffnm ${MDRUN_NAME}
-# analysis
-# Create analysis output directory
+
+# extra ndx file , select protein
+echo -e "1\nq" | gmx_mpi make_ndx -f ${MDRUN_NAME}.gro -o ${NDX_FILE}
+# echo -e "1\nq" | gmx_mpi make_ndx -f md.gro -o index.ndx
+
+# Create extraction output directory
 mkdir -p ${OUTPUT_FOLDER}
 
+# Create temp output directory
+mkdir -p ${TEMP_FOLDER}
+
+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
+
+# echo -e "1\nq" | gmx_mpi trjconv -dt 100 -s md.tpr -f md.xtc -n index.ndx -pbc mol -o temp/temp.xtc
+
+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
+
+# 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
+
+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
+
+# 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
+
+# Group     1 (        Protein) 
+
+# ---
+# Step 1: Extract frames every 1000 ps
+gmx_mpi trjconv -s ${TPR_FILE} -f ${XTC_FILE} -o ${OUTPUT_FOLDER}/${NO_PBC_XTC_FILE} -dt ${EXTRACT_EVERY_PS} -pbc mol <<EOF
+0
+EOF
+
+# Step 2: Center and fit the trajectory
+# Centering the protein and fitting to the initial frame
+gmx_mpi trjconv -s ${TPR_FILE} -f ${OUTPUT_FOLDER}/${NO_PBC_XTC_FILE} -o ${OUTPUT_FOLDER}/${NO_PBC_XTC_FILE} -pbc mol -center <<EOF
+1
+1
+EOF
+
+# Step 3: Output PDB format file
+gmx_mpi trjconv -s ${TPR_FILE} -f ${OUTPUT_FOLDER}/${NO_PBC_XTC_FILE} -o ${OUTPUT_FOLDER}/${MDRUN_NAME}.pdb -pbc mol -center <<EOF
+1
+0
+EOF
+
+# Continue with further analysis like RMSD calculation...
+# ... [other analysis commands] ...
+
+# End of script
+
+# command reference
+
 # Command 1: 提取蛋白质
 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'
 # echo "Protein": 选择蛋白质组，用于告诉 gmx trjconv 要处理哪个部分。
@@ -280,27 +330,4 @@ command_2 = f'echo "Protein\nProtein\nProtein" | gmx trjconv -s {tpr_file} -f {t
 # Command 3: 抽取帧生成 .pdb 文件
 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'
 # -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。
-# -o {output_folder}/tarj_show.pdb: 输出为 .pdb 格式，存储在指定的位置。
-
-# Step 1: Extract frames every 1000 ps
-gmx_mpi trjconv -s ${TPR_FILE} -f ${XTC_FILE} -o ${OUTPUT_FOLDER}/${NO_PBC_XTC_FILE} -dt ${EXTRACT_EVERY_PS} -pbc mol <<EOF
-0
-EOF
-
-# Step 2: Center and fit the trajectory
-# Centering the protein and fitting to the initial frame
-gmx_mpi trjconv -s ${TPR_FILE} -f ${OUTPUT_FOLDER}/${NO_PBC_XTC_FILE} -o ${OUTPUT_FOLDER}/${NO_PBC_XTC_FILE} -pbc mol -center <<EOF
-1
-0
-EOF
-
-# Step 3: Output PDB format file
-gmx_mpi trjconv -s ${TPR_FILE} -f ${OUTPUT_FOLDER}/${NO_PBC_XTC_FILE} -o ${OUTPUT_FOLDER}/${MDRUN_NAME}.pdb -pbc mol -center <<EOF
-1
-0
-EOF
-
-# Continue with further analysis like RMSD calculation...
-# ... [other analysis commands] ...
-
-# End of script
+# -o {output_folder}/tarj_show.pdb: 输出为 .pdb 格式，存储在指定的位置。