Re: Aoid protein to reach periodic boundary

From: Jeff Comer (
Date: Tue Jan 12 2016 - 09:30:36 CST

In addition to what Jerome said, you seem to misunderstand periodic
boundary conditions. The periodic boundary is only apparent—there is no
boundary! Your simulation should work perfectly well whether you restrain
the protein to the middle or not. For visualization, you can wrap the
trajectory later using pbctools in VMD.


Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

On Mon, Jan 11, 2016 at 6:15 PM, 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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