if im not mistaken, i remembered it as violin concerto in d minor ...
but the closest thing per this website, is this one...
"Prelude (From the Unaccompanied Cello Suite No. 1 in G Major, BWV 1007)"
Composed by Johann Sebastian Bach
Performed by Yo-Yo Ma, cello
Courtesy of Sony Classical
By Arrangement with Sony Music Licensing
http://www.imdb.com/title/tt0311113/soundtrack
Track listing
1. The far Side of the World (09:19)
2. Into the Fog (02:12)
3. Violin Concerto No. 3 "Strassburg" K.216, 3rd Movement (01:20)
by Wolfgang Amadeus Mozart
4. The Cuckold comes out of the Amery (03:27)
Traditional
5. Smoke n'Oakum (05:28)
6. Fantasia on a Theme by Thomas Tallis (05:15)
by Ralph Vaughan Williams
7. Adagio from Concerto Grosso Op. 6, No. 8 in G Minor (01:57)
by Arcangelo Corelli
8. The Doldrums (02:46)
9. Prelude (from the unaccompanied Cello Suite No. 1 in G Major, BWV 1007) (02:28)
by Johann Sebastian Bach
10. The Galapagos (01:39)
11. Folk Medley (05:13)
Traditional
- O'Sullivan's March
- The Cuckold comes out of the Amery
- Mother Hen
- Mary Scott
- Nancy Dawson
12. The Phasmid (02:35)
13. The Battle (05:08)
14. La Musica notturna delle Strade di Madrid, No. 6, Op. 30 (09:23)
by Luigi Boccherini
15. Full Circle (01:35)
http://www.soundtrackcollector.com/title/60157/Master+And+Commander:+The+Far+Side+Of+The+World