The particular prayer that your grandfather once prayed to calm storms at sea will be rather hard to pinpoint as there are many saints invoked against storms and this list is not a complete one. Both St. Michael the Archangel and St. Nicholas of Myra are traditionally invoked against storms at sea. St. Peter is one of the patron saint of fishermen. As you see there is a large list in play and we may never know for sure.
I will give here three hopeful possibilities, but before going into detail I would like to mention the Scriptures tell us that Our Lord (Matthew 8:24-28) and the Prophet Jonah (Jonah 1:11-12) both calmed storms at sea and could be invoked as the need presents. The Prophet Jonah is honoured on September 21 in the Roman Martyrology.
The most popular saint invoked against storms is St. Scholastica (February 10). In Malta, there is a unique feast in St. Paul the Apostle's honour known as the Shipwreck of St. Paul (Naufragium S. Pauli), which is also held on the 10th of February. How St. Scholastica became invoked against storms can be found here. In times of real necessity the short prayers are the easiest to recite.
St. Scholastica and St. Paul the Apostle, pray for us.
My second suggestion is the traditional prayer to repel dangerous storms taken from the missal of 1962. I personally use these sort of prayers in my own private devotional life accompanied with St. Scholastica.
When a major storm is headed your way, you should prepare as much as you can. But you should also pray.
Prayer is powerful, and it can change history. No, we don’t always get what we prayed for. But God always hears us – and sometimes he does grant us what we pray for.
These prayers, titled “Ad Repellendas Tempestates” (“To Repel Storms”), are meant to be used in the extraordinary form of the Mass at their respective parts (and some people are using them!). But feel free to use them as inspiration for your own personal prayer.
Here’s the original Latin:
A domo tua, quǽsumus, Dómine, spiritales nequítiæ, repellantur: et aërearum discédat malígnitas tempestatum. Per Dóminum.
And here’s an English translation:
We beseech Thee, O Lord, that all wickedness being driven away from Thy house, the fury of the raging tempest may pass away. Through our Lord.
The Traditional Catholic Mass Prayers to Repel Dangerous Storms
My last suggestion is a prayer to St. Medard.
Prayer against tornadoes?
I am not aware of any specific prayer against tornadoes, but I do know that St. Medard is traditionally regarded as the patron saint against bad weather. He was a bishop in France during the first half of the sixth century.
Legend has it that when he was a child, he was once sheltered from a violent rainstorm by an eagle that hovered over his head. That is how he is commonly depicted in art, and Christians have long invoked his aid in stormy weather.
The prayer that is said admits of different versions but generally goes something like this:
“Lord Jesus, though the intercession of St. Medard, be with me during the storms of my life and the storms of nature. Protect the victims of hurricanes, tornadoes, earthquakes and other natural disasters. Send in helpers and multiply the supplies that are needed for their aid. You calmed the storm on the Sea of Galilee; deliver us now from the storms that rage around us. Amen.”