#!/bin/bash

# 执行回旋半径分析
gmx_mpi gyrate -s ${MDRUN_NAME}.tpr -n index.ndx -f ${MDRUN_NAME}_center.xtc -o gyration_protein.xvg << EOF
1  # 选择 Protein 进行回旋半径分析
EOF

# 使用 Gnuplot 生成回旋半径分析图像
gnuplot << EOF
set terminal svg size 800,600
set output 'gyration_protein.svg'

# 设置标题和轴标签
set title 'Radius of Gyration Analysis'
set xlabel 'Time (ns)'
set ylabel 'Radius of Gyration (nm)'

# 读取数据文件并绘制
plot 'gyration_protein.xvg' using 1:2 with lines title 'Rg (nm)'
EOF

echo "Gyration plot generated: gyration_protein.svg"