update

md_gromacs.sh

@@ -4,27 +4,48 @@
 # reference: http://www.mdtutorials.com/gmx/lysozyme/
 # NAME=1ao7 NSTEPS=50000000 ./md_gromacs.sh  
 # 命令会临时设置 NAME 为 1ao7 和 NSTEPS 为 50000000（对应 100ns），然后运行 md_gromacs.sh 脚本
-NAME="5sws_fixer"
-FORCEFIELD="amber99sb-ildn"
-WATERMODEL="tip3p"
-WATERTOPFILE="spc216.gro"
-BOXTYPE="tric"
-BOXORIENTATION="1.0"
+# Check if GMXRC_PATH is provided and source it
+if [ -n "$GMXRC_PATH" ]; then
+    source "$GMXRC_PATH" # source /home/lingyuzeng/software/gmx2023.2/bin/GMXRC
+fi
+NAME=${NAME:-"5sws_fixer"}
+FORCEFIELD=${FORCEFIELD:-"amber99sb-ildn"}
+WATERMODEL=${WATERMODEL:-"tip3p"}
+WATERTOPFILE=${WATERTOPFILE:-"spc216.gro"}
+BOXTYPE=${BOXTYPE:-"tric"}
+BOXORIENTATION=${BOXORIENTATION:-"1.0"}
 NSTEPS=${NSTEPS:-500000} # 50,000 steps for 1 ns
 DT=${DT:-0.002} # 2 fs
 #BOXSIZE="5.0"
 #BOXCENTER="2.5"
 # Define simulation name variable
-MDRUN_NAME="md"
+MDRUN_NAME=${MDRUN_NAME:-"md"}
 # Define analysis parameters
 # Define other filenames based on MDRUN_NAME
 TPR_FILE="${MDRUN_NAME}.tpr"
 XTC_FILE="${MDRUN_NAME}.xtc"
 NO_PBC_XTC_FILE="${MDRUN_NAME}_noPBC.xtc"
-OUTPUT_FOLDER="analysis_results"
+OUTPUT_FOLDER=${OUTPUT_FOLDER:-"analysis_results"}
 # Define variables for frame extraction
 EXTRACT_EVERY_PS=${EXTRACT_EVERY_PS:-1000} # Default to 1000 ps if not set
-# source /home/lingyuzeng/software/gmx2023.2/bin/GMXRC
+
+# Print the current settings
+echo "Current settings:"
+echo "NAME: $NAME"
+echo "FORCEFIELD: $FORCEFIELD"
+echo "WATERMODEL: $WATERMODEL"
+echo "WATERTOPFILE: $WATERTOPFILE"
+echo "BOXTYPE: $BOXTYPE"
+echo "BOXORIENTATION: $BOXORIENTATION"
+echo "NSTEPS: $NSTEPS"
+echo "DT: $DT"
+echo "MDRUN_NAME: $MDRUN_NAME"
+echo "TPR_FILE: $TPR_FILE"
+echo "XTC_FILE: $XTC_FILE"
+echo "NO_PBC_XTC_FILE: $NO_PBC_XTC_FILE"
+echo "OUTPUT_FOLDER: $OUTPUT_FOLDER"
+echo "EXTRACT_EVERY_PS: $EXTRACT_EVERY_PS"
+
 # generate GROMACS .gro file
 gmx_mpi pdb2gmx -f $NAME.pdb -o $NAME.gro -ff $FORCEFIELD -water $WATERMODEL -ignh -p topol.top
 # define the box