MS氢键计算脚本

VMD统计氢不能统计PBC（周期性边界条件）。

HBondStats.pl脚本内容如下：

#!perl

# Purpose: Calculate statistics (Min/Max/Mean) on the Hydrogen Bonds
#            in a structure. Put the results in a Study Table.

use strict;
use warnings;
use MaterialsScript qw(:all);

#Initialize variables for the stats calculations
my $totalLength = 0;
my $minLength   = 99999.9; #Arbitrary Big Num
my $maxLength   = 0;
my $row = 0;

#Get all the HBonds in the UnitCell
my $hbonds = $Documents{"urea.xsd"}->UnitCell->HydrogenBonds;

#Create a new Study Table for the results
my $statsDoc = Documents->New("HBondStats.std");

foreach my $hbond (@$hbonds) {
#Output the bond length for each HBond
$statsDoc->Cell($row, 0) = "HBond $row";
$statsDoc->Cell($row, 1) = $hbond->Length;

#Update the statistics information
$totalLength += $hbond->Length;

if($hbond->Length < $minLength) {
$minLength = $hbond->Length;
}
elsif($hbond->Length > $maxLength) {
$maxLength = $hbond->Length;
}

++$row;
}

#printout the overall statistics
$statsDoc->Cell($row, 0) = "Average";
$statsDoc->Cell($row, 1) = $totalLength/$row;
$statsDoc->Cell($row, 2) = "Min";
$statsDoc->Cell($row, 3) = $minLength;
$statsDoc->Cell($row, 4) = "Max";
$statsDoc->Cell($row, 5) = $maxLength;

将17行的urea.xsd改为需要统计的文件名。

File->import导入perl脚本。

运行脚本。

出现报错：42行除数等于0。

检查后发现因为氢键总数为0，所以$row变量的值也为初始值0。

原因是运行脚本前没有calculate hydrogen bond，计算一下重新运行脚本。

最终输出结果如下：