Aoid protein to reach periodic boundary

From: Dharmeshkumar Patel (
Date: Mon Jan 11 2016 - 18:15:16 CST


I am simulating protein in water box at high temperature and longer period of time. My aim is to observe protein unfolding. I can see the start of unfolding but once protein reached to periodic boundary then it stuck there and unfolding process stopped. So I put colvar COM restraint as suggested by others in the group but with this restraint unfolding process didn't start even though i put 0.1Kcal/mol COM restraint. I even increased water box size but it didn't work. Is there any way i can stop protein to reach to periodic boundary? I would really appreciate your suggestions.


Dharmeshkumar Patel,
PhD Research Scholar,
University of Sydney,

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