Re: protein unfolding

From: Axel Kohlmeyer (
Date: Thu Jan 21 2010 - 08:15:10 CST

On Thu, Jan 21, 2010 at 8:29 AM, jose correa <> wrote:
> Dear all
> We are trying to unfolding a protein employing thermal conditions (300, 400,
> 500 and 600 K). I was thinking that at 600 K the protein was unfolded, but,

i assume that you are aware of the fact that at 600K parameters
that were derived for 300K have limited applicability.

> it did not happen. I start heating the sytem from equilibration and then, I
> matain the system under NTV. Do you have any suggestion?.

how long did you run? what kind of system? how large of a protein?
how large is your solvation box relative to the size of the protein?

depending on the rigidity of your system, it may take a while to break up
a structure. also you need to allow for fluctuations, i.e. give the protein
some "wiggle room" to ease the process.


> Best wishes
> José Correa-Basurto
> ESM-IPN, México

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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