VMD计算原子到面的最短距离，TCL脚本

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已于 2024-11-07 11:23:09 修改

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文章标签：算法

于 2024-11-07 11:14:37 首次发布

本文链接：https://blog.csdn.net/weixin_44620047/article/details/143589422

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#calculate the distance between atom and planes in the trajectory# 

 set result [open dist-h-mental.txt w]
 set nframe [molinfo top get numframes]
 #目标原子
 set p [atomselect top "index 48"]
 #组成平面的三个原子
 set a [atomselect top "index 44"]
 set b [atomselect top "index 45"]
 set c [atomselect top "index 46"]
 set sum 0
 #遍历每一帧
 for {set i 0} {$i<$nframe} {incr i 1} {
 $p frame $i
 $a frame $i
 $b frame $i
 $c frame $i
 $p update
 $a update
 $b update
 $c update
 #计算向量 ba 和 bc
 set vecba [vecsub [measure center $b] [measure center $a]]
 set vecbc [vecsub [measure center $b] [measure center $c]]
 #计算法向量及其长度
 set normal [veccross $vecba $vecbc ]
 set normal_length [veclength $normal]
 #计算向量pa
 set target_to_plane [vecsub [measure center $p] [measure center $a]]
 #计算距离
 set distance [ expr abs([vecdot $target_to_plane $normal]) / $normal_length]
 puts $result "$i $distance"
 set sum [expr $sum+$distance]
 }
 close $result
 puts "the average diatance is : [expr double($sum)/$nframe]"