按照您的思路，成功了，谢谢sob老师。下面是我在您的基础上修改的TCL文件，适用于实时显示偶极矩方向：

proc showdip {args} {
global vmd_frame
graphics 0 delete all
set sel [atomselect top all frame $vmd_frame(0)]
set dir [measure dipole $sel -debye]
set com [measure center $sel weight mass]
scan $dir "%f %f %f" x1 y1 z1
scan $com "%f %f %f" x0 y0 z0
set end "[expr $x0+$x1] [expr $y0+$y1] [expr $z0+$z1]"
set init "[expr $x0] [expr $y0] [expr $z0]"
puts "com = $init"
puts "end = $end"
puts "dip = $dir"
graphics 0 color red
graphics 0 cylinder $init $end radius 0.3 filled yes resolution 20
$sel delete
}

# trace variable vmd_frame(0) w showdip
# trace vdelete vmd_frame(0) w showdi

先把原子电荷读入VMD作为原子的charge属性
然后建立一个回调函数，帧数每切换一次就自动调用一次回调函数，计算偶极矩、删除原有物体并绘制出新的箭头

部分内容可参考
使VMD实时显示gromacs轨迹中原子的受力
http://sobereva.com/36