Re: Aoid protein to reach periodic boundary

From: Felipe Merino (
Date: Tue Jan 12 2016 - 06:13:43 CST


I might be missing something here. If you are using a periodic system
then reaching the edge of the box is irrelevant, unless the protein
starts to interact with any of its copies. As Jerome mention above you
should just wait some time for the protein to
break, which will depend in the actual temperature you use, the
stability of your protein, etc.


On 12/01/16 12:41, Branko wrote:
> Patel,
> 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
> Branko
> 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*

Felipe Merino
Max Planck Institute for Molecular Physiology
Department of Structural Biochemistry
Otto-Hahn-Str. 11
44227 Dortmund
Phone: +49 231 133 2315

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