MS计算轨迹的分子间作用能

最新推荐文章于 2024-08-26 15:01:02 发布

lisa25496

最新推荐文章于 2024-08-26 15:01:02 发布

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分类专栏： MS

本文链接：https://blog.csdn.net/qq_31346429/article/details/109352645

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之前写过一篇关于计算分子间作用能的文章，那如何计算轨迹的分子间相互作用能呢？此时，需要利用perl脚本进行计算。

MS的help已经给出了计算单个xsd文件相互作用能的脚本，我们需要做的就是将它进一步优化，用于轨迹文件分子间作用能的计算。主要思想包括以下几个部分：（1）提取各个Layer,用于后面的计算（2）计算各个Layer能量及总能量（3）采用循环语句，循环（1）（2）步

1 创建列表 这是所有工作之前的准备工作，需要创建一个列表存储layer和计算数据

my $doc = $Documents{"Layer.xtd"};
my $newStudyTable = Documents->New("InteractionEnergy.std");
my $calcSheet = $newStudyTable->ActiveSheet;
# 创建列表抬头
$calcSheet->ColumnHeading(0) = "Cell";
$calcSheet->ColumnHeading(1) = "Total Energy of Cell";
$calcSheet->ColumnHeading(2) = "layer1";
$calcSheet->ColumnHeading(3) = "Energy of layer1";
$calcSheet->ColumnHeading(4) = "layer2";
$calcSheet->ColumnHeading(5) = "Energy of layer2";

2 提取各个Layer

my $layer1Doc = Documents->New("bottom.xsd");
my $layer2Doc = Documents->New("top.xsd");
	
$allDoc->CopyFrom($doc);
$layer1Doc->CopyFrom($doc);
$layer1Doc->UnitCell->Sets("Layer 2")->Atoms->Delete; 
$layer2Doc->CopyFrom($doc);
$layer2Doc->UnitCell->Sets("Layer 1")->Atoms->Delete; 
		
#取消所有原子的固定
my $atoms = $allDoc->UnitCell->Atoms;
$atoms->Unfix("XYZ");
my $atoms = $layer1Doc->UnitCell->Atoms;
$atoms->Unfix("XYZ");	
	
#将结构放到表格对应的位置
$calcSheet->Cell($counter-1,0) = $allDoc;
$calcSheet->Cell($counter-1,2) = $layer1Doc;
$calcSheet->Cell($counter-1,4) = $layer2Doc;

3 能量计算 首先是基本参数设置，然后进行计算。其中，由于有一步是删除计算后的.xsd文件，这是因为计算过程中会产生大量的过程文件，这样可以防止内存不够。

#首先是forcite的设置，这一步你可以直接打开forcite，设置完所有选项后粘贴过来
my $forcite = Modules->Forcite;
$forcite->ChangeSettings(Settings(Quality => "Fine",
	CurrentForcefield => "COMPASS"));

#计算每个layer的能量及总能量
$forcite->Energy->Run($allDoc);
$calcSheet->Cell($counter-1, 1) = $allDoc->PotentialEnergy; 
$forcite->Energy->Run($layer1Doc);
$calcSheet->Cell($counter-1, 3) = $layer1Doc->PotentialEnergy; 
$forcite->Energy->Run($layer2Doc);
$calcSheet->Cell($counter-1, 5) = $layer2Doc->PotentialEnergy; 

$calcSheet->Cell($counter-1,0) = $allDoc-> UnitCell->Atoms->Delete; 
$calcSheet->Cell($counter-1,2) = $layer1Doc-> UnitCell->Atoms->Delete;
$calcSheet->Cell($counter-1,4) = $layer2Doc-> UnitCell->Atoms->Delete;

my $interactionEnergy = $totalEnergy - ($layer1Energy + $layer2Energy);
$calcSheet->Cell($counter-1, 6) = $interactionEnergy;

#删除过程文件
my $totalEnergy = $calcSheet->Cell($counter-1, 1);
my $layer1Energy = $calcSheet->Cell($counter-1, 3);
my $layer2Energy = $calcSheet->Cell($counter-1, 5);

4循环计算 以轨迹的帧数为循环次数，设定自己的循环步长，然后将计算主体塞入循环即可

my $numFrames = $doc->Trajectory->NumFrames;
for (my $counter = 1; $counter <= $numFrames ; ++$counter) {
	#sets the current frame to the value of counter
	$doc->Trajectory->CurrentFrame = $counter;
	...循环主体...
}