Re: Aoid protein to reach periodic boundary

From: Jérôme Hénin (
Date: Tue Jan 12 2016 - 05:34:22 CST


The COM restraint should not prevent unfolding, or interfere with it in any
way. Something else muse be happening - possibly just random fluctuations,
ie. the unfolding process may start eventually if you give it enough time.
Either that, or something else changed other than the COM restraint.


On 12 January 2016 at 01:15, 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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