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Goalscoring defender Joe Martin admitted the Gills were fortunate to come away from Colchester with a win.
Martin and his fellow team-mates were overworked in the second half as Colchester laid siege to the Gillingham goal.
But despite the pressure, the Essex hosts were unable to get the goals they needed.
Martin, who scored Gills’ first goal in the 2-1 win, said: “There was a little disappointment from our second half performance but obviously we are delighted with the win.
“It was a really important game for us to win but we can’t play like we did in the second half too often and expect to get a win. We have to make sure our performances are a bit better in the future.
“It is not always about playing well though. It is a results business and we are delighted with the three points.”
Martin struck home from Cody McDonald’s cross to end a free-flowing move with a goal.
“The boys did great to get down the side,” said Martin.
“I saw Cody’s ball come over and I knew I was going to have an opportunity to make a connection. Thankfully it was good because I didn’t want to mess the move up.”
Bradley Dack combined with McDonald to score the second but a goal early in the second half from Colchester made it tense.
“We didn’t start right and we knew the third goal was going to be important,” Martin said.
“As soon as they got that goal their tails went up and the second half was difficult for us. We need to make sure in future we start right in every half.
“We got a little bit lucky at times but we will take that. We’ll scrap this one and look to the next game now.”
Next up for the Gills is a home game against Bristol City on Sunday.
“It will be a tough game,” said the left-back, who now had two goals to his name this season.
“They are a good side and we haven’t got any pressure on us. They We will hopefully make it difficult for them and get a result.”