upate

process_xtc.sh

@@ -14,7 +14,19 @@ mkdir -p "$OUTPUT_FOLDER"
 # 文件路径
 INDEX_FILE="${INPUT_FOLDER}/index.ndx"
 TPR_FILE="${INPUT_FOLDER}/md.tpr"
-XTC_FILE="${INPUT_FOLDER}/md.xtc"
+
+#  提取索引文件
+echo "q" | gmx_mpi make_ndx -f ${PDB_FILE} -o index.ndx
+
+# step 0: Remove water and output a new XTC file
+echo "Remove water and output a new XTC file" | gmx_mpi trjconv -s ${TPR_FILE} -f ${XTC_FILE} -o ${TEMP_FOLDER}/no_water.xtc -pbc mol
+
+# Center the protein in the trajectory
+echo "Protein" | gmx_mpi trjconv -s ${TPR_FILE} -f ${TEMP_FOLDER}/no_water.xtc -o ${TEMP_FOLDER}/centered.xtc -center -pbc mol
+
+# Extract frames every 1000 ps from the centered trajectory and output to a PDB file
+echo "Protein" | gmx_mpi trjconv -s ${TPR_FILE} -f ${TEMP_FOLDER}/centered.xtc -o ${OUTPUT_FOLDER}/${MDRUN_NAME}.pdb -dt ${EXTRACT_EVERY_PS} -pbc mol -center
+
 
 # 提取ndx文件
 echo -e "Protein\nq\n" | gmx make_ndx -f 5sws_fixer.pdb -o index.ndx