"I think (the Inter game) is more difficult now than before this decision because I am a relationship coach, the players have a social and emotional relationship with me and my staff," he told reporters on Monday ahead of Tuesday's last 16 tie.
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Bayern take a 1-0 lead into the home leg over the holders after a last-gasp victory in the San Siro last month and are fresh from a 6-0 rout of Hamburg SV on Saturday, after which many players said they felt "liberated".
However Van Gaal reiterated that last week's news of the joint decision to terminate his contract, due to finish in 2012, was still on the players' minds.
"These emotional ties are now under greater pressure.
"A professional must always be focused on the game but it is not always easy. Everything has an influence on a player and their daily form and how they work with other players."
In order to advance, Inter, who beat Bayern 2-0 in last season's final, must become only the second team in Champions League history to overturn a first leg home defeat with a second leg away win.
"The UEFA people told me so far only one team have managed it. So statistically we have the advantage," said the 59-year-old, who looked relaxed and even enjoyed a joke with his player Mario Gomez.
"In what minute will you score," asked Van Gaal.
"What minute would you like me to score, coach?" replied Gomez, who was on target in the 90th minute to give Bayern a precious away win in the San Siro.
