Re: Aoid protein to reach periodic boundary

From: Branko (
Date: Tue Jan 12 2016 - 05:41:21 CST


try to fix position of two atoms in protein which are near of its
center of mass. In this way you will stop 'moving' of protein within
your water cluster


On 1/12/2016 1:15 AM, Dharmeshkumar Patel wrote:
> Hi,
> 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.
> Thanks,
> *Dharmeshkumar Patel,
> PhD Research Scholar,
> University of Sydney,
> Sydney*

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