标题: 求助VMD如何添加周期性边界条件计算原子间距 [打印本页] 作者Author: MXM 时间: 2021-8-6 19:03 标题: 求助VMD如何添加周期性边界条件计算原子间距 大家好，我想用VMD后处理得到周期性结构里面两个原子之间的距离变化情况，自己参考https://www.ks.uiuc.edu/Research ... st/vmd-l/27057.html 的脚本运行了一下，但是报错，missing operator at _@_ in expression "...0359296798706 + (6/2) _@_6) - (6/2)"
(parsing expression "pmodulo( -1.3447715044...")invoked from within"expr pmodulo( $x1 - $x2 + ($boxX/2) $boxX) - ($boxX/2)"
("for" body line 26)
初学TCL，不知道怎么解决，麻烦大家帮忙看看：
package require pbctools
pbc set {6 6 8} -all
set outfile [open "test.dat" w]
set nf [molinfo top get numframes]
set ind24 [atomselect top "index 24"]
set ind32 [atomselect top "index 32"]
set boxX 6
set boxY 6
set boxZ 8
for {set i 0} {$i < $nf} {incr i} {
$ind24 frame $i
$ind32 frame $i
set x1 [$ind24 get {x}]
set y1 [$ind24 get {y}]
set z1 [$ind24 get {z}]
set x2 [$ind32 get {x}]
set y2 [$ind32 get {y}]
set z2 [$ind32 get {z}]
proc pmodulo {n m} {
return [expr $n - $m * floor(1.0 * $n/$m)]
}
set Dx [expr pmodulo( $x1 - $x2 + ($boxX/2) $boxX) - ($boxX/2)]
set Dy [expr pmodulo( $y1 - $y2 + ($boxY/2) $boxY) - ($boxY/2)]
set Dz [expr pmodulo( $z1 - $z2 + ($boxZ/2) $boxZ) - ($boxZ/2)]
set D [expr sqrt( ($Dx * $Dx) + ($Dy * $Dy) + ($Dz * $Dz) )]
puts $outfile "$i \t $D "
}
close $outfile