In 1951, he was sent to Arzamas-16, also known as KB-11 (English: Design Bureau-11), now the All-Russian Scientific Research Institute of Experimental Physics (VNIIEF), in the closed city of Sarov, Nizhny Novgorod Oblast.

He was one of the main authors of the final report concerning the configuration and feasibility calculations of the RDS-37, which was detonated successfully a few months later in November 1955.

He then worked on 'Project 49', with Yuri Babayev, which involved technical improvements in the implosion of the two-stage charges, which were tested successfully in 1958 and put into production.

Yevgeny Avrorin described Trutnev producing the first "clean" nuclear charge, "a purely thermonuclear reaction" from a solid compound.

[7][8] Employees at Arzamas-16, including Trutnev, were upset that on a visit by Edward Teller and Siegfried S. Hecker (then director of the Los Alamos National Laboratory) to Russia after the break-up of the USSR, each was photographed in front of a model of the RDS-220 alongside scientists in Snezhinsk.