<?php
$productId = Mage::getModel('catalog/product')->getIdBySku('sku');
$product = Mage::getModel('catalog/product')->load($productId);
$productId1 = 1;
$productId2 = 2;
$relatedLinks = array();
$relatedLinks[$productId1] = array('position'=>'') ;
$relatedLinks[$productId2] = array('position'=>'') ;
$product->setRelatedLinkData($relatedLinks);
?>